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Diff for /imach/src/imach.c between versions 1.125 and 1.295

-version 1.125, 2006/04/04 15:20:31
+version 1.295, 2019/05/18 09:52:50
  Line 1
  /* $Id$
    $State$
    $Log$
+   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: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
    Revision 1.125  2006/04/04 15:20:31  lievre
    Errors in calculation of health expectancies. Age was not initialized.
    Forecasting file added.
    Revision 1.124  2006/03/22 17:13:53  lievre
    Parameters are printed with %lf instead of %f (more numbers after the comma).
    The log-likelihood is printed in the log file
    Revision 1.123  2006/03/20 10:52:43  brouard
    * imach.c (Module): <title> changed, corresponds to .htm file
    name. <head> headers where missing.
    * imach.c (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.122  2006/03/20 09:45:41  brouard
    (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.121  2006/03/16 17:45:01  lievre
    * imach.c (Module): Comments concerning covariates added
    * imach.c (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.120  2006/03/16 15:10:38  lievre
    (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.119  2006/03/15 17:42:26  brouard
    (Module): Bug if status = -2, the loglikelihood was
    computed as likelihood omitting the logarithm. Version O.98e
    Revision 1.118  2006/03/14 18:20:07  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.117  2006/03/14 17:16:22  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.116  2006/03/06 10:29:27  brouard
    (Module): Variance-covariance wrong links and
    varian-covariance of ej. is needed (Saito).
    Revision 1.115  2006/02/27 12:17:45  brouard
    (Module): One freematrix added in mlikeli! 0.98c
    Revision 1.114  2006/02/26 12:57:58  brouard
    (Module): Some improvements in processing parameter
    filename with strsep.
    Revision 1.113  2006/02/24 14:20:24  brouard
    (Module): Memory leaks checks with valgrind and:
    datafile was not closed, some imatrix were not freed and on matrix
    allocation too.
    Revision 1.112  2006/01/30 09:55:26  brouard
    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    Revision 1.111  2006/01/25 20:38:18  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    (Module): Comments can be added in data file. Missing date values
    can be a simple dot '.'.
    Revision 1.110  2006/01/25 00:51:50  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    Revision 1.109  2006/01/24 19:37:15  brouard
    (Module): Comments (lines starting with a #) are allowed in data.
    Revision 1.108  2006/01/19 18:05:42  lievre
    Gnuplot problem appeared...
    To be fixed
    Revision 1.107  2006/01/19 16:20:37  brouard
    Test existence of gnuplot in imach path
    Revision 1.106  2006/01/19 13:24:36  brouard
    Some cleaning and links added in html output
    Revision 1.105  2006/01/05 20:23:19  lievre
    *** empty log message ***
    Revision 1.104  2005/09/30 16:11:43  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    (Module): If the status is missing at the last wave but we know
    that the person is alive, then we can code his/her status as -2
    (instead of missing=-1 in earlier versions) and his/her
    contributions to the likelihood is 1 - Prob of dying from last
    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    the healthy state at last known wave). Version is 0.98
    Revision 1.103  2005/09/30 15:54:49  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    Revision 1.102  2004/09/15 17:31:30  brouard
    Add the possibility to read data file including tab characters.
    Revision 1.101  2004/09/15 10:38:38  brouard
    Fix on curr_time
    Revision 1.100  2004/07/12 18:29:06  brouard
    Add version for Mac OS X. Just define UNIX in Makefile
    Revision 1.99  2004/06/05 08:57:40  brouard
    *** empty log message ***
    Revision 1.98  2004/05/16 15:05:56  brouard
    New version 0.97 . First attempt to estimate force of mortality
    directly from the data i.e. without the need of knowing the health
    state at each age, but using a Gompertz model: log u =a + b*age .
    This is the basic analysis of mortality and should be done before any
    other analysis, in order to test if the mortality estimated from the
    cross-longitudinal survey is different from the mortality estimated
    from other sources like vital statistic data.
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
    the slope with 95% confident intervals.
    Current limitations:
    A) Even if you enter covariates, i.e. with the
    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    B) There is no computation of Life Expectancy nor Life Table.
    Revision 1.97  2004/02/20 13:25:42  lievre
    Version 0.96d. Population forecasting command line is (temporarily)
    suppressed.
    Revision 1.96  2003/07/15 15:38:55  brouard
    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs.
    Revision 1.95  2003/07/08 07:54:34  brouard
    * imach.c (Repository):
    (Repository): Using imachwizard code to output a more meaningful covariance
    matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
    Revision 1.93  2003/06/25 16:33:55  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    (Module): Version 0.96b
    Revision 1.92  2003/06/25 16:30:45  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    Revision 1.91  2003/06/25 15:30:29  brouard
    * imach.c (Repository): Duplicated warning errors corrected.
    (Repository): Elapsed time after each iteration is now output. It
    helps to forecast when convergence will be reached. Elapsed time
    is stamped in powell.  We created a new html file for the graphs
    concerning matrix of covariance. It has extension -cov.htm.
    Revision 1.90  2003/06/24 12:34:15  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.88  2003/06/23 17:54:56  brouard
    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    Revision 1.87  2003/06/18 12:26:01  brouard
    Version 0.96
    Revision 1.86  2003/06/17 20:04:08  brouard
    (Module): Change position of html and gnuplot routines and added
    routine fileappend.
    Revision 1.85  2003/06/17 13:12:43  brouard
    * imach.c (Repository): Check when date of death was earlier that
    current date of interview. It may happen when the death was just
    prior to the death. In this case, dh was negative and likelihood
    was wrong (infinity). We still send an "Error" but patch by
    assuming that the date of death was just one stepm after the
    interview.
    (Repository): Because some people have very long ID (first column)
    we changed int to long in num[] and we added a new lvector for
    memory allocation. But we also truncated to 8 characters (left
    truncation)
    (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
    Revision 1.82  2003/06/05 15:57:20  brouard
    Add log in  imach.c and  fullversion number is now printed.
  */
  /*
     Interpolated Markov Chain
    Short summary of the programme:
-   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
-   convergence.
+   have a more complex model than "constant and age", you should modify
+   the program where the markup *Covariates have to be included here
-   The advantage of this computer programme, compared to a simple
+   again* invites you to do it.  More covariates you add, slower the
-   multinomial logistic model, is clear when the delay between waves is not
+   convergence.
-   identical for each individual. Also, if a individual missed an
-   intermediate interview, the information is lost, but taken into
+   The advantage of this computer programme, compared to a simple
-   account using an interpolation or extrapolation.
+   multinomial logistic model, is clear when the delay between waves is not
+   identical for each individual. Also, if a individual missed an
-   hPijx is the probability to be observed in state i at age x+h
+   intermediate interview, the information is lost, but taken into
-   conditional to the observed state i at age x. The delay 'h' can be
+   account using an interpolation or extrapolation.
-   split into an exact number (nh*stepm) of unobserved intermediate
-   states. This elementary transition (by month, quarter,
+   hPijx is the probability to be observed in state i at age x+h
-   semester or year) is modelled as a multinomial logistic.  The hPx
+   conditional to the observed state i at age x. The delay 'h' can be
-   matrix is simply the matrix product of nh*stepm elementary matrices
+   split into an exact number (nh*stepm) of unobserved intermediate
-   and the contribution of each individual to the likelihood is simply
+   states. This elementary transition (by month, quarter,
-   hPijx.
+   semester or year) is modelled as a multinomial logistic.  The hPx
+   matrix is simply the matrix product of nh*stepm elementary matrices
-   Also this programme outputs the covariance matrix of the parameters but also
+   and the contribution of each individual to the likelihood is simply
-   of the life expectancies. It also computes the period (stable) prevalence.
+   hPijx.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Also this programme outputs the covariance matrix of the parameters but also
-            Institut national d'�tudes d�mographiques, Paris.
+   of the life expectancies. It also computes the period (stable) prevalence.
-   This software have been partly granted by Euro-REVES, a concerted action
-   from the European Union.
+ Back prevalence and projections:
-   It is copyrighted identically to a GNU software product, ie programme and
-   software can be distributed freely for non commercial use. Latest version
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
-   can be accessed at http://euroreves.ined.fr/imach .
+    double agemaxpar, double ftolpl, int *ncvyearp, double
+    dateprev1,double dateprev2, int firstpass, int lastpass, int
-   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
+    mobilavproj)
-   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
+     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,
-   main
-   read parameterfile
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
-   read datafile
+        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
-   concatwav
-   freqsummary
+    - hBijx Back Probability to be in state i at age x-h being in j at x
-   if (mle >= 1)
+    Computes for any combination of covariates k and any age between bage and fage
-     mlikeli
+    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   print results files
+                         oldm=oldms;savm=savms;
-   if mle==1
-      computes hessian
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
-   read end of parameter file: agemin, agemax, bage, fage, estepm
+      Computes the transition matrix starting at age 'age' over
-       begin-prev-date,...
+      'nhstepm*hstepm*stepm' months (i.e. until
-   open gnuplot file
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   open html file
+      nhstepm*hstepm matrices.
-   period (stable) prevalence
-    for age prevalim()
+      Returns p3mat[i][j][h] after calling
-   h Pij x
+      p3mat[i][j][h]=matprod2(newm,
-   variance of p varprob
+      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
-   forecasting if prevfcast==1 prevforecast call prevalence()
+      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-   health expectancies
+      oldm);
-   Variance-covariance of DFLE
-   prevalence()
+ Important routines
-    movingaverage()
-   varevsij()
+ - func (or funcone), computes logit (pij) distinguishing
-   if popbased==1 varevsij(,popbased)
+   o fixed variables (single or product dummies or quantitative);
-   total life expectancies
+   o varying variables by:
-   Variance of period (stable) prevalence
+    (1) wave (single, product dummies, quantitative),
-  end
+    (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
- #include <math.h>
+   o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
- #include <stdio.h>
+     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
- #include <stdlib.h>
- #include <string.h>
- #include <unistd.h>
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
- #include <limits.h>
+            Institut national d'études démographiques, Paris.
- #include <sys/types.h>
+   This software have been partly granted by Euro-REVES, a concerted action
- #include <sys/stat.h>
+   from the European Union.
- #include <errno.h>
+   It is copyrighted identically to a GNU software product, ie programme and
- extern int errno;
+   software can be distributed freely for non commercial use. Latest version
+   can be accessed at http://euroreves.ined.fr/imach .
- /* #include <sys/time.h> */
- #include <time.h>
+   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
- #include "timeval.h"
+   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
- /* #include <libintl.h> */
+   **********************************************************************/
- /* #define _(String) gettext (String) */
+ /*
+   main
- #define MAXLINE 256
+   read parameterfile
+   read datafile
- #define GNUPLOTPROGRAM "gnuplot"
+   concatwav
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+   freqsummary
- #define FILENAMELENGTH 132
+   if (mle >= 1)
+     mlikeli
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+   print results files
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+   if mle==1
+      computes hessian
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+   read end of parameter file: agemin, agemax, bage, fage, estepm
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+       begin-prev-date,...
+   open gnuplot file
- #define NINTERVMAX 8
+   open html file
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
- #define NCOVMAX 8 /* Maximum number of covariates */
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
- #define MAXN 20000
+     freexexit2 possible for memory heap.
- #define YEARM 12. /* Number of months per year */
- #define AGESUP 130
+   h Pij x                         | pij_nom  ficrestpij
- #define AGEBASE 40
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
- #ifdef UNIX
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
- #define DIRSEPARATOR '/'
- #define CHARSEPARATOR "/"
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
- #define ODIRSEPARATOR '\\'
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
- #else
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
- #define DIRSEPARATOR '\\'
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- #define CHARSEPARATOR "\\"
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
- #define ODIRSEPARATOR '/'
- #endif
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
- /* $Id$ */
+   Variance-covariance of DFLE
- /* $State$ */
+   prevalence()
+    movingaverage()
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+   varevsij()
- char fullversion[]="$Revision$ $Date$";
+   if popbased==1 varevsij(,popbased)
- char strstart[80];
+   total life expectancies
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+   Variance of period (stable) prevalence
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+  end
- int nvar;
+ */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
- int npar=NPARMAX;
+ /* #define DEBUG */
- int nlstate=2; /* Number of live states */
+ /* #define DEBUGBRENT */
- int ndeath=1; /* Number of dead states */
+ /* #define DEBUGLINMIN */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ /* #define DEBUGHESS */
- int popbased=0;
+ #define DEBUGHESSIJ
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define POWELL /* Instead of NLOPT */
- int maxwav; /* Maxim number of waves */
+ #define POWELLNOF3INFF1TEST /* Skip test */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #include <math.h>
- int mle, weightopt;
+ #include <stdio.h>
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #include <stdlib.h>
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #include <string.h>
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #include <ctype.h>
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double jmean; /* Mean space between 2 waves */
+ #ifdef _WIN32
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #include <io.h>
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #include <windows.h>
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #include <tchar.h>
- FILE *ficlog, *ficrespow;
+ #else
- int globpr; /* Global variable for printing or not */
+ #include <unistd.h>
- double fretone; /* Only one call to likelihood */
+ #endif
- long ipmx; /* Number of contributions */
- double sw; /* Sum of weights */
+ #include <limits.h>
- char filerespow[FILENAMELENGTH];
+ #include <sys/types.h>
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- FILE *ficresilk;
+ #if defined(__GNUC__)
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- FILE *ficresprobmorprev;
+ #endif
- FILE *fichtm, *fichtmcov; /* Html File */
- FILE *ficreseij;
+ #include <sys/stat.h>
- char filerese[FILENAMELENGTH];
+ #include <errno.h>
- FILE *ficresstdeij;
+ /* extern int errno; */
- char fileresstde[FILENAMELENGTH];
- FILE *ficrescveij;
+ /* #ifdef LINUX */
- char filerescve[FILENAMELENGTH];
+ /* #include <time.h> */
- FILE  *ficresvij;
+ /* #include "timeval.h" */
- char fileresv[FILENAMELENGTH];
+ /* #else */
- FILE  *ficresvpl;
+ /* #include <sys/time.h> */
- char fileresvpl[FILENAMELENGTH];
+ /* #endif */
- char title[MAXLINE];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ #include <time.h>
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ #ifdef GSL
- char command[FILENAMELENGTH];
+ #include <gsl/gsl_errno.h>
- int  outcmd=0;
+ #include <gsl/gsl_multimin.h>
+ #endif
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- char filelog[FILENAMELENGTH]; /* Log file */
+ #ifdef NLOPT
- char filerest[FILENAMELENGTH];
+ #include <nlopt.h>
- char fileregp[FILENAMELENGTH];
+ typedef struct {
- char popfile[FILENAMELENGTH];
+   double (* function)(double [] );
+ } myfunc_data ;
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ #endif
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ /* #include <libintl.h> */
- struct timezone tzp;
+ /* #define _(String) gettext (String) */
- extern int gettimeofday();
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- long time_value;
- extern long time();
+ #define GNUPLOTPROGRAM "gnuplot"
- char strcurr[80], strfor[80];
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #define FILENAMELENGTH 132
- char *endptr;
- long lval;
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- double dval;
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define NR_END 1
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- #define FREE_ARG char*
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- #define FTOL 1.0e-10
+ #define NINTERVMAX 8
- #define NRANSI
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- #define ITMAX 200
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
+ #define NCOVMAX 20  /**< Maximum number of covariates, including generated covariates V1*V2 */
- #define TOL 2.0e-4
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
- #define CGOLD 0.3819660
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- #define ZEPS 1.0e-10
+ /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ #define YEARM 12. /**< Number of months per year */
+ /* #define AGESUP 130 */
- #define GOLD 1.618034
+ /* #define AGESUP 150 */
- #define GLIMIT 100.0
+ #define AGESUP 200
- #define TINY 1.0e-20
+ #define AGEINF 0
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
- static double maxarg1,maxarg2;
+ #define AGEBASE 40
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #define AGEOVERFLOW 1.e20
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
+ #ifdef _WIN32
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ #define DIRSEPARATOR '\\'
- #define rint(a) floor(a+0.5)
+ #define CHARSEPARATOR "\\"
+ #define ODIRSEPARATOR '/'
- static double sqrarg;
+ #else
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define DIRSEPARATOR '/'
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ #define CHARSEPARATOR "/"
- int agegomp= AGEGOMP;
+ #define ODIRSEPARATOR '\\'
+ #endif
- int imx;
- int stepm=1;
+ /* $Id$ */
- /* Stepm, step in month: minimum step interpolation*/
+ /* $State$ */
+ #include "version.h"
- int estepm;
+ char version[]=__IMACH_VERSION__;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
+ char fullversion[]="$Revision$ $Date$";
- int m,nb;
+ char strstart[80];
- long *num;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- double **pmmij, ***probs;
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- double *ageexmed,*agecens;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- double dateintmean=0;
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
- double *weight;
+ int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
- int **s; /* Status */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- double *agedc, **covar, idx;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- double *lsurv, *lpop, *tpop;
+ 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 */
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
- double ftolhess; /* Tolerance for computing hessian */
+ int nsd=0; /**< Total number of single dummy variables (output) */
+ int nsq=0; /**< Total number of single quantitative variables (output) */
- /**************** split *************************/
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
- {
+ int ntveff=0; /**< ntveff number of effective time varying variables */
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ int cptcov=0; /* Working variable */
-   */
+ int nobs=10;  /* Number of observations in the data lastobs-firstobs */
-   char  *ss;                            /* pointer */
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
-   int   l1, l2;                         /* length counters */
+ int npar=NPARMAX;
+ int nlstate=2; /* Number of live states */
-   l1 = strlen(path );                   /* length of path */
+ int ndeath=1; /* Number of dead states */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ int popbased=0;
-     strcpy( name, path );               /* we got the fullname name because no directory */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ int *wav; /* Number of waves for this individuual 0 is possible */
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ int maxwav=0; /* Maxim number of waves */
-     /* get current working directory */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
-       return( GLOCK_ERROR_GETCWD );
+                    to the likelihood and the sum of weights (done by funcone)*/
-     }
+ int mle=1, weightopt=0;
-     /* got dirc from getcwd*/
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
-     printf(" DIRC = %s \n",dirc);
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
-   } else {                              /* strip direcotry from path */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
-     ss++;                               /* after this, the filename */
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
-     l2 = strlen( ss );                  /* length of filename */
+ int countcallfunc=0;  /* Count the number of calls to func */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
-     strcpy( name, ss );         /* save file name */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ double jmean=1; /* Mean space between 2 waves */
-     dirc[l1-l2] = 0;                    /* add zero */
+ double **matprod2(); /* test */
-     printf(" DIRC2 = %s \n",dirc);
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
-   }
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-   /* We add a separator at the end of dirc if not exists */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
-   l1 = strlen( dirc );                  /* length of directory */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ /*FILE *fic ; */ /* Used in readdata only */
-     dirc[l1] =  DIRSEPARATOR;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
-     dirc[l1+1] = 0;
+ FILE *ficlog, *ficrespow;
-     printf(" DIRC3 = %s \n",dirc);
+ int globpr=0; /* Global variable for printing or not */
-   }
+ double fretone; /* Only one call to likelihood */
-   ss = strrchr( name, '.' );            /* find last / */
+ long ipmx=0; /* Number of contributions */
-   if (ss >0){
+ double sw; /* Sum of weights */
-     ss++;
+ char filerespow[FILENAMELENGTH];
-     strcpy(ext,ss);                     /* save extension */
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
-     l1= strlen( name);
+ FILE *ficresilk;
-     l2= strlen(ss)+1;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
-     strncpy( finame, name, l1-l2);
+ FILE *ficresprobmorprev;
-     finame[l1-l2]= 0;
+ FILE *fichtm, *fichtmcov; /* Html File */
-   }
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
-   return( 0 );                          /* we're done */
+ FILE *ficresstdeij;
- }
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
- /******************************************/
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- void replace_back_to_slash(char *s, char*t)
- {
+ char title[MAXLINE];
-   int i;
+ char model[MAXLINE]; /**< The model line */
-   int lg=0;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
-   i=0;
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
-   lg=strlen(t);
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
-   for(i=0; i<= lg; i++) {
+ char command[FILENAMELENGTH];
-     (s[i] = t[i]);
+ int  outcmd=0;
-     if (t[i]== '\\') s[i]='/';
-   }
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- }
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
+ char filelog[FILENAMELENGTH]; /* Log file */
- int nbocc(char *s, char occ)
+ char filerest[FILENAMELENGTH];
- {
+ char fileregp[FILENAMELENGTH];
-   int i,j=0;
+ char popfile[FILENAMELENGTH];
-   int lg=20;
-   i=0;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
-   lg=strlen(s);
-   for(i=0; i<= lg; i++) {
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
-   if  (s[i] == occ ) j++;
+ /* struct timezone tzp; */
-   }
+ /* extern int gettimeofday(); */
-   return j;
+ struct tm tml, *gmtime(), *localtime();
- }
+ extern time_t time();
- void cutv(char *u,char *v, char*t, char occ)
- {
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ struct tm tm;
-      gives u="abcedf" and v="ghi2j" */
-   int i,lg,j,p=0;
+ char strcurr[80], strfor[80];
-   i=0;
-   for(j=0; j<=strlen(t)-1; j++) {
+ char *endptr;
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ long lval;
-   }
+ double dval;
-   lg=strlen(t);
+ #define NR_END 1
-   for(j=0; j<p; j++) {
+ #define FREE_ARG char*
-     (u[j] = t[j]);
+ #define FTOL 1.0e-10
-   }
-      u[p]='\0';
+ #define NRANSI
+ #define ITMAX 200
-    for(j=0; j<= lg; j++) {
+ #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
-   }
+ #define TOL 2.0e-4
- }
+ #define CGOLD 0.3819660
- /********************** nrerror ********************/
+ #define ZEPS 1.0e-10
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- void nrerror(char error_text[])
- {
+ #define GOLD 1.618034
-   fprintf(stderr,"ERREUR ...\n");
+ #define GLIMIT 100.0
-   fprintf(stderr,"%s\n",error_text);
+ #define TINY 1.0e-20
-   exit(EXIT_FAILURE);
- }
+ static double maxarg1,maxarg2;
- /*********************** vector *******************/
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
- double *vector(int nl, int nh)
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- {
-   double *v;
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ #define rint(a) floor(a+0.5)
-   if (!v) nrerror("allocation failure in vector");
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-   return v-nl+NR_END;
+ #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 */
- /************************ free vector ******************/
+ /* static double dsqrarg; */
- void free_vector(double*v, int nl, int nh)
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
- {
+ static double sqrarg;
-   free((FREE_ARG)(v+nl-NR_END));
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
- }
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
- /************************ivector *******************************/
- int *ivector(long nl,long nh)
+ int imx;
- {
+ int stepm=1;
-   int *v;
+ /* Stepm, step in month: minimum step interpolation*/
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   if (!v) nrerror("allocation failure in ivector");
+ int estepm;
-   return v-nl+NR_END;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- }
+ int m,nb;
- /******************free ivector **************************/
+ long *num;
- void free_ivector(int *v, long nl, long nh)
+ int firstpass=0, lastpass=4,*cod, *cens;
- {
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
-   free((FREE_ARG)(v+nl-NR_END));
+                    covariate for which somebody answered excluding
- }
+                    undefined. Usually 2: 0 and 1. */
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
- /************************lvector *******************************/
+                              covariate for which somebody answered including
- long *lvector(long nl,long nh)
+                              undefined. Usually 3: -1, 0 and 1. */
- {
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-   long *v;
+ double **pmmij, ***probs; /* Global pointer */
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ double ***mobaverage, ***mobaverages; /* New global variable */
-   if (!v) nrerror("allocation failure in ivector");
+ double *ageexmed,*agecens;
-   return v-nl+NR_END;
+ double dateintmean=0;
- }
+ double *weight;
- /******************free lvector **************************/
+ int **s; /* Status */
- void free_lvector(long *v, long nl, long nh)
+ double *agedc;
- {
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   free((FREE_ARG)(v+nl-NR_END));
+                   * covar=matrix(0,NCOVMAX,1,n);
- }
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
+ double **coqvar; /* Fixed quantitative covariate nqv */
- /******************* imatrix *******************************/
+ double ***cotvar; /* Time varying covariate ntv */
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+ double ***cotqvar; /* Time varying quantitative covariate itqv */
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ double  idx;
- {
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-   int **m;
+ /*k          1  2   3   4     5    6    7     8    9 */
+ /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
-   /* allocate pointers to rows */
+ /* Tndvar[k]    1   2   3               4          5 */
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+ /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
-   m += NR_END;
+ /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
-   m -= nrl;
+ /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+ /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
-   /* allocate rows and set pointers to them */
+ /* Tprod[i]=k           4               7            */
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ /* Tage[i]=k                  5               8      */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /* */
-   m[nrl] += NR_END;
+ /* Type                    */
-   m[nrl] -= ncl;
+ /* V         1  2  3  4  5 */
+ /*           F  F  V  V  V */
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ /*           D  Q  D  D  Q */
+ /*                         */
-   /* return pointer to array of pointers to rows */
+ int *TvarsD;
-   return m;
+ int *TvarsDind;
- }
+ int *TvarsQ;
+ int *TvarsQind;
- /****************** free_imatrix *************************/
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ #define MAXRESULTLINES 10
-       int **m;
+ int nresult=0;
-       long nch,ncl,nrh,nrl;
+ int parameterline=0; /* # of the parameter (type) line */
-      /* free an int matrix allocated by imatrix() */
+ int TKresult[MAXRESULTLINES];
- {
+ int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
-   free((FREE_ARG) (m+nrl-NR_END));
+ int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
- }
+ double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
- /******************* matrix *******************************/
+ int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
- double **matrix(long nrl, long nrh, long ncl, long nch)
- {
+ /* 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 *\/ */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ 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 */
-   double **m;
+ 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 */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ 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 */
-   m += NR_END;
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-   m -= nrl;
+ 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 */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   m[nrl] += NR_END;
+ int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   m[nrl] -= ncl;
+ 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 */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ 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 */
-   return m;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ 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 */
- /*************************free matrix ************************/
+ 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 */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
- {
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ int *Tage;
-   free((FREE_ARG)(m+nrl-NR_END));
+ 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*/
- /******************* ma3x *******************************/
+ 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  */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ int *Ndum; /** Freq of modality (tricode */
- {
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ int **Tvard;
-   double ***m;
+ int *Tprod;/**< Gives the k position of the k1 product */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ int *Tposprod; /**< Gives the k1 product from the k position */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
-   m += NR_END;
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
-   m -= nrl;
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
+ double *lsurv, *lpop, *tpop;
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ #define FD 1; /* Fixed dummy covariate */
-   m[nrl] += NR_END;
+ #define FQ 2; /* Fixed quantitative covariate */
-   m[nrl] -= ncl;
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ #define VD 10; /* Varying dummy covariate */
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ #define VQ 11; /* Varying quantitative covariate */
-   m[nrl][ncl] += NR_END;
+ #define VP 12; /* Varying product covariate */
-   m[nrl][ncl] -= nll;
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
-   for (j=ncl+1; j<=nch; j++)
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
-   for (i=nrl+1; i<=nrh; i++) {
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ #define APVD 18; /* Age product * varying dummy covariate */
-     for (j=ncl+1; j<=nch; j++)
+ #define APVQ 19; /* Age product * varying quantitative covariate */
-       m[i][j]=m[i][j-1]+nlay;
-   }
+ #define FTYPE 1; /* Fixed covariate */
-   return m;
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   */
+ struct kmodel{
- }
+         int maintype; /* main type */
+         int subtype; /* subtype */
- /*************************free ma3x ************************/
+ };
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ struct kmodel modell[NCOVMAX];
- {
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ double ftolhess; /**< Tolerance for computing hessian */
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ /**************** split *************************/
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- /*************** function subdirf ***********/
+ {
- char *subdirf(char fileres[])
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
- {
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   /* Caution optionfilefiname is hidden */
+   */
-   strcpy(tmpout,optionfilefiname);
+   char  *ss;                            /* pointer */
-   strcat(tmpout,"/"); /* Add to the right */
+   int   l1=0, l2=0;                             /* length counters */
-   strcat(tmpout,fileres);
-   return tmpout;
+   l1 = strlen(path );                   /* length of path */
- }
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- /*************** function subdirf2 ***********/
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
- char *subdirf2(char fileres[], char *preop)
+     strcpy( name, path );               /* we got the fullname name because no directory */
- {
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   /* Caution optionfilefiname is hidden */
+     /* get current working directory */
-   strcpy(tmpout,optionfilefiname);
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   strcat(tmpout,"/");
+ #ifdef WIN32
-   strcat(tmpout,preop);
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   strcat(tmpout,fileres);
+ #else
-   return tmpout;
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
- }
+ #endif
+       return( GLOCK_ERROR_GETCWD );
- /*************** function subdirf3 ***********/
+     }
- char *subdirf3(char fileres[], char *preop, char *preop2)
+     /* got dirc from getcwd*/
- {
+     printf(" DIRC = %s \n",dirc);
+   } else {                              /* strip directory from path */
-   /* Caution optionfilefiname is hidden */
+     ss++;                               /* after this, the filename */
-   strcpy(tmpout,optionfilefiname);
+     l2 = strlen( ss );                  /* length of filename */
-   strcat(tmpout,"/");
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   strcat(tmpout,preop);
+     strcpy( name, ss );         /* save file name */
-   strcat(tmpout,preop2);
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   strcat(tmpout,fileres);
+     dirc[l1-l2] = '\0';                 /* add zero */
-   return tmpout;
+     printf(" DIRC2 = %s \n",dirc);
- }
+   }
+   /* We add a separator at the end of dirc if not exists */
- /***************** f1dim *************************/
+   l1 = strlen( dirc );                  /* length of directory */
- extern int ncom;
+   if( dirc[l1-1] != DIRSEPARATOR ){
- extern double *pcom,*xicom;
+     dirc[l1] =  DIRSEPARATOR;
- extern double (*nrfunc)(double []);
+     dirc[l1+1] = 0;
+     printf(" DIRC3 = %s \n",dirc);
- double f1dim(double x)
+   }
- {
+   ss = strrchr( name, '.' );            /* find last / */
-   int j;
+   if (ss >0){
-   double f;
+     ss++;
-   double *xt;
+     strcpy(ext,ss);                     /* save extension */
+     l1= strlen( name);
-   xt=vector(1,ncom);
+     l2= strlen(ss)+1;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+     strncpy( finame, name, l1-l2);
-   f=(*nrfunc)(xt);
+     finame[l1-l2]= 0;
-   free_vector(xt,1,ncom);
+   }
-   return f;
- }
+   return( 0 );                          /* we're done */
+ }
- /*****************brent *************************/
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- {
+ /******************************************/
-   int iter;
-   double a,b,d,etemp;
+ void replace_back_to_slash(char *s, char*t)
-   double fu,fv,fw,fx;
+ {
-   double ftemp;
+   int i;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   int lg=0;
-   double e=0.0;
+   i=0;
+   lg=strlen(t);
-   a=(ax < cx ? ax : cx);
+   for(i=0; i<= lg; i++) {
-   b=(ax > cx ? ax : cx);
+     (s[i] = t[i]);
-   x=w=v=bx;
+     if (t[i]== '\\') s[i]='/';
-   fw=fv=fx=(*f)(x);
+   }
-   for (iter=1;iter<=ITMAX;iter++) {
+ }
-     xm=0.5*(a+b);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ char *trimbb(char *out, char *in)
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-     printf(".");fflush(stdout);
+   char *s;
-     fprintf(ficlog,".");fflush(ficlog);
+   s=out;
- #ifdef DEBUG
+   while (*in != '\0'){
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+       in++;
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+     }
- #endif
+     *out++ = *in++;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   }
-       *xmin=x;
+   *out='\0';
-       return fx;
+   return s;
-     }
+ }
-     ftemp=fu;
-     if (fabs(e) > tol1) {
+ /* char *substrchaine(char *out, char *in, char *chain) */
-       r=(x-w)*(fx-fv);
+ /* { */
-       q=(x-v)*(fx-fw);
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
-       p=(x-v)*q-(x-w)*r;
+ /*   char *s, *t; */
-       q=2.0*(q-r);
+ /*   t=in;s=out; */
-       if (q > 0.0) p = -p;
+ /*   while ((*in != *chain) && (*in != '\0')){ */
-       q=fabs(q);
+ /*     *out++ = *in++; */
-       etemp=e;
+ /*   } */
-       e=d;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+ /*   /\* *in matches *chain *\/ */
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
-       else {
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-         d=p/q;
+ /*   } */
-         u=x+d;
+ /*   in--; chain--; */
-         if (u-a < tol2 || b-u < tol2)
+ /*   while ( (*in != '\0')){ */
-           d=SIGN(tol1,xm-x);
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-       }
+ /*     *out++ = *in++; */
-     } else {
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /*   } */
-     }
+ /*   *out='\0'; */
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ /*   out=s; */
-     fu=(*f)(u);
+ /*   return out; */
-     if (fu <= fx) {
+ /* } */
-       if (u >= x) a=x; else b=x;
+ char *substrchaine(char *out, char *in, char *chain)
-       SHFT(v,w,x,u)
+ {
-         SHFT(fv,fw,fx,fu)
+   /* Substract chain 'chain' from 'in', return and output 'out' */
-         } else {
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
-           if (u < x) a=u; else b=u;
-           if (fu <= fw || w == x) {
+   char *strloc;
-             v=w;
-             w=u;
+   strcpy (out, in);
-             fv=fw;
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
-             fw=fu;
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
-           } else if (fu <= fv || v == x || v == w) {
+   if(strloc != NULL){
-             v=u;
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
-             fv=fu;
+     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);
-   nrerror("Too many iterations in brent");
+   return out;
-   *xmin=x;
+ }
-   return fx;
- }
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- /****************** mnbrak ***********************/
+ {
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-             double (*func)(double))
+      gives blocc="abcdef" and alocc="ghi2j".
- {
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-   double ulim,u,r,q, dum;
+   */
-   double fu;
+   char *s, *t;
+   t=in;s=in;
-   *fa=(*func)(*ax);
+   while ((*in != occ) && (*in != '\0')){
-   *fb=(*func)(*bx);
+     *alocc++ = *in++;
-   if (*fb > *fa) {
+   }
-     SHFT(dum,*ax,*bx,dum)
+   if( *in == occ){
-       SHFT(dum,*fb,*fa,dum)
+     *(alocc)='\0';
-       }
+     s=++in;
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   }
-   *fc=(*func)(*cx);
-   while (*fb > *fc) {
+   if (s == t) {/* occ not found */
-     r=(*bx-*ax)*(*fb-*fc);
+     *(alocc-(in-s))='\0';
-     q=(*bx-*cx)*(*fb-*fa);
+     in=s;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   }
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   while ( *in != '\0'){
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+     *blocc++ = *in++;
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   }
-       fu=(*func)(u);
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+   *blocc='\0';
-       fu=(*func)(u);
+   return t;
-       if (fu < *fc) {
+ }
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-           SHFT(*fb,*fc,fu,(*func)(u))
+ {
-           }
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-       u=ulim;
+      gives blocc="abcdef2ghi" and alocc="j".
-       fu=(*func)(u);
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-     } else {
+   */
-       u=(*cx)+GOLD*(*cx-*bx);
+   char *s, *t;
-       fu=(*func)(u);
+   t=in;s=in;
-     }
+   while (*in != '\0'){
-     SHFT(*ax,*bx,*cx,u)
+     while( *in == occ){
-       SHFT(*fa,*fb,*fc,fu)
+       *blocc++ = *in++;
-       }
+       s=in;
- }
+     }
+     *blocc++ = *in++;
- /*************** linmin ************************/
+   }
+   if (s == t) /* occ not found */
- int ncom;
+     *(blocc-(in-s))='\0';
- double *pcom,*xicom;
+   else
- double (*nrfunc)(double []);
+     *(blocc-(in-s)-1)='\0';
+   in=s;
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   while ( *in != '\0'){
- {
+     *alocc++ = *in++;
-   double brent(double ax, double bx, double cx,
+   }
-                double (*f)(double), double tol, double *xmin);
-   double f1dim(double x);
+   *alocc='\0';
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   return s;
-               double *fc, double (*func)(double));
+ }
-   int j;
-   double xx,xmin,bx,ax;
+ int nbocc(char *s, char occ)
-   double fx,fb,fa;
+ {
+   int i,j=0;
-   ncom=n;
+   int lg=20;
-   pcom=vector(1,n);
+   i=0;
-   xicom=vector(1,n);
+   lg=strlen(s);
-   nrfunc=func;
+   for(i=0; i<= lg; i++) {
-   for (j=1;j<=n;j++) {
+     if  (s[i] == occ ) j++;
-     pcom[j]=p[j];
+   }
-     xicom[j]=xi[j];
+   return j;
-   }
+ }
-   ax=0.0;
-   xx=1.0;
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ /* { */
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- #ifdef DEBUG
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ /*   int i,lg,j,p=0; */
- #endif
+ /*   i=0; */
-   for (j=1;j<=n;j++) {
+ /*   lg=strlen(t); */
-     xi[j] *= xmin;
+ /*   for(j=0; j<=lg-1; j++) { */
-     p[j] += xi[j];
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   }
+ /*   } */
-   free_vector(xicom,1,n);
-   free_vector(pcom,1,n);
+ /*   for(j=0; j<p; j++) { */
- }
+ /*     (u[j] = t[j]); */
+ /*   } */
- char *asc_diff_time(long time_sec, char ascdiff[])
+ /*      u[p]='\0'; */
- {
-   long sec_left, days, hours, minutes;
+ /*    for(j=0; j<= lg; j++) { */
-   days = (time_sec) / (60*60*24);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   sec_left = (time_sec) % (60*60*24);
+ /*   } */
-   hours = (sec_left) / (60*60) ;
+ /* } */
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
+ #ifdef _WIN32
-   sec_left = (sec_left) % (60);
+ char * strsep(char **pp, const char *delim)
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ {
-   return ascdiff;
+   char *p, *q;
- }
+   if ((p = *pp) == NULL)
- /*************** powell ************************/
+     return 0;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   if ((q = strpbrk (p, delim)) != NULL)
-             double (*func)(double []))
+   {
- {
+     *pp = q + 1;
-   void linmin(double p[], double xi[], int n, double *fret,
+     *q = '\0';
-               double (*func)(double []));
+   }
-   int i,ibig,j;
+   else
-   double del,t,*pt,*ptt,*xit;
+     *pp = 0;
-   double fp,fptt;
+   return p;
-   double *xits;
+ }
-   int niterf, itmp;
+ #endif
-   pt=vector(1,n);
+ /********************** nrerror ********************/
-   ptt=vector(1,n);
-   xit=vector(1,n);
+ void nrerror(char error_text[])
-   xits=vector(1,n);
+ {
-   *fret=(*func)(p);
+   fprintf(stderr,"ERREUR ...\n");
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   fprintf(stderr,"%s\n",error_text);
-   for (*iter=1;;++(*iter)) {
+   exit(EXIT_FAILURE);
-     fp=(*fret);
+ }
-     ibig=0;
+ /*********************** vector *******************/
-     del=0.0;
+ double *vector(int nl, int nh)
-     last_time=curr_time;
+ {
-     (void) gettimeofday(&curr_time,&tzp);
+   double *v;
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+   if (!v) nrerror("allocation failure in vector");
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+   return v-nl+NR_END;
-    for (i=1;i<=n;i++) {
+ }
-       printf(" %d %.12f",i, p[i]);
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+ /************************ free vector ******************/
-       fprintf(ficrespow," %.12lf", p[i]);
+ void free_vector(double*v, int nl, int nh)
-     }
+ {
-     printf("\n");
+   free((FREE_ARG)(v+nl-NR_END));
-     fprintf(ficlog,"\n");
+ }
-     fprintf(ficrespow,"\n");fflush(ficrespow);
-     if(*iter <=3){
+ /************************ivector *******************************/
-       tm = *localtime(&curr_time.tv_sec);
+ int *ivector(long nl,long nh)
-       strcpy(strcurr,asctime(&tm));
+ {
- /*       asctime_r(&tm,strcurr); */
+   int *v;
-       forecast_time=curr_time;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-       itmp = strlen(strcurr);
+   if (!v) nrerror("allocation failure in ivector");
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   return v-nl+NR_END;
-         strcurr[itmp-1]='\0';
+ }
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+ /******************free ivector **************************/
-       for(niterf=10;niterf<=30;niterf+=10){
+ void free_ivector(int *v, long nl, long nh)
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ {
-         tmf = *localtime(&forecast_time.tv_sec);
+   free((FREE_ARG)(v+nl-NR_END));
- /*      asctime_r(&tmf,strfor); */
+ }
-         strcpy(strfor,asctime(&tmf));
-         itmp = strlen(strfor);
+ /************************lvector *******************************/
-         if(strfor[itmp-1]=='\n')
+ long *lvector(long nl,long nh)
-         strfor[itmp-1]='\0';
+ {
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   long *v;
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-       }
+   if (!v) nrerror("allocation failure in ivector");
-     }
+   return v-nl+NR_END;
-     for (i=1;i<=n;i++) {
+ }
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       fptt=(*fret);
+ /******************free lvector **************************/
- #ifdef DEBUG
+ void free_lvector(long *v, long nl, long nh)
-       printf("fret=%lf \n",*fret);
+ {
-       fprintf(ficlog,"fret=%lf \n",*fret);
+   free((FREE_ARG)(v+nl-NR_END));
- #endif
+ }
-       printf("%d",i);fflush(stdout);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+ /******************* imatrix *******************************/
-       linmin(p,xit,n,fret,func);
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-       if (fabs(fptt-(*fret)) > del) {
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-         del=fabs(fptt-(*fret));
+ {
-         ibig=i;
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-       }
+   int **m;
- #ifdef DEBUG
-       printf("%d %.12e",i,(*fret));
+   /* allocate pointers to rows */
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-       for (j=1;j<=n;j++) {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   m += NR_END;
-         printf(" x(%d)=%.12e",j,xit[j]);
+   m -= nrl;
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       }
-       for(j=1;j<=n;j++) {
+   /* allocate rows and set pointers to them */
-         printf(" p=%.12e",p[j]);
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-         fprintf(ficlog," p=%.12e",p[j]);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       }
+   m[nrl] += NR_END;
-       printf("\n");
+   m[nrl] -= ncl;
-       fprintf(ficlog,"\n");
- #endif
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     }
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   /* return pointer to array of pointers to rows */
- #ifdef DEBUG
+   return m;
-       int k[2],l;
+ }
-       k[0]=1;
-       k[1]=-1;
+ /****************** free_imatrix *************************/
-       printf("Max: %.12e",(*func)(p));
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       int **m;
-       for (j=1;j<=n;j++) {
+       long nch,ncl,nrh,nrl;
-         printf(" %.12e",p[j]);
+      /* free an int matrix allocated by imatrix() */
-         fprintf(ficlog," %.12e",p[j]);
+ {
-       }
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-       printf("\n");
+   free((FREE_ARG) (m+nrl-NR_END));
-       fprintf(ficlog,"\n");
+ }
-       for(l=0;l<=1;l++) {
-         for (j=1;j<=n;j++) {
+ /******************* matrix *******************************/
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ {
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-         }
+   double **m;
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       }
+   if (!m) nrerror("allocation failure 1 in matrix()");
- #endif
+   m += NR_END;
+   m -= nrl;
-       free_vector(xit,1,n);
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       free_vector(xits,1,n);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       free_vector(ptt,1,n);
+   m[nrl] += NR_END;
-       free_vector(pt,1,n);
+   m[nrl] -= ncl;
-       return;
-     }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+   return m;
-     for (j=1;j<=n;j++) {
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-       ptt[j]=2.0*p[j]-pt[j];
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-       xit[j]=p[j]-pt[j];
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-       pt[j]=p[j];
+    */
-     }
+ }
-     fptt=(*func)(ptt);
-     if (fptt < fp) {
+ /*************************free matrix ************************/
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-       if (t < 0.0) {
+ {
-         linmin(p,xit,n,fret,func);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-         for (j=1;j<=n;j++) {
+   free((FREE_ARG)(m+nrl-NR_END));
-           xi[j][ibig]=xi[j][n];
+ }
-           xi[j][n]=xit[j];
-         }
+ /******************* ma3x *******************************/
- #ifdef DEBUG
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-         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);
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-         for(j=1;j<=n;j++){
+   double ***m;
-           printf(" %.12e",xit[j]);
-           fprintf(ficlog," %.12e",xit[j]);
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-         }
+   if (!m) nrerror("allocation failure 1 in matrix()");
-         printf("\n");
+   m += NR_END;
-         fprintf(ficlog,"\n");
+   m -= nrl;
- #endif
-       }
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-     }
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   }
+   m[nrl] += NR_END;
- }
+   m[nrl] -= ncl;
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
- {
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   m[nrl][ncl] += NR_END;
-      matrix by transitions matrix until convergence is reached */
+   m[nrl][ncl] -= nll;
+   for (j=ncl+1; j<=nch; j++)
-   int i, ii,j,k;
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   double min, max, maxmin, maxmax,sumnew=0.;
-   double **matprod2();
+   for (i=nrl+1; i<=nrh; i++) {
-   double **out, cov[NCOVMAX], **pmij();
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   double **newm;
+     for (j=ncl+1; j<=nch; j++)
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+       m[i][j]=m[i][j-1]+nlay;
+   }
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   return m;
-     for (j=1;j<=nlstate+ndeath;j++){
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-     }
+   */
+ }
-    cov[1]=1.;
+ /*************************free ma3x ************************/
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ {
-     newm=savm;
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-     /* Covariates have to be included here again */
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-      cov[2]=agefin;
+   free((FREE_ARG)(m+nrl-NR_END));
+ }
-       for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ /*************** function subdirf ***********/
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+ char *subdirf(char fileres[])
-       }
+ {
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   /* Caution optionfilefiname is hidden */
-       for (k=1; k<=cptcovprod;k++)
+   strcpy(tmpout,optionfilefiname);
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   strcat(tmpout,"/"); /* Add to the right */
+   strcat(tmpout,fileres);
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   return tmpout;
-       /*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]);*/
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
-     savm=oldm;
+ {
-     oldm=newm;
-     maxmax=0.;
+   /* Caution optionfilefiname is hidden */
-     for(j=1;j<=nlstate;j++){
+   strcpy(tmpout,optionfilefiname);
-       min=1.;
+   strcat(tmpout,"/");
-       max=0.;
+   strcat(tmpout,preop);
-       for(i=1; i<=nlstate; i++) {
+   strcat(tmpout,fileres);
-         sumnew=0;
+   return tmpout;
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+ }
-         prlim[i][j]= newm[i][j]/(1-sumnew);
-         max=FMAX(max,prlim[i][j]);
+ /*************** function subdirf3 ***********/
-         min=FMIN(min,prlim[i][j]);
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-       }
+ {
-       maxmin=max-min;
-       maxmax=FMAX(maxmax,maxmin);
+   /* Caution optionfilefiname is hidden */
-     }
+   strcpy(tmpout,optionfilefiname);
-     if(maxmax < ftolpl){
+   strcat(tmpout,"/");
-       return prlim;
+   strcat(tmpout,preop);
-     }
+   strcat(tmpout,preop2);
-   }
+   strcat(tmpout,fileres);
- }
+   return tmpout;
+ }
- /*************** transition probabilities ***************/
+ /*************** function subdirfext ***********/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ char *subdirfext(char fileres[], char *preop, char *postop)
  {
-   double s1, s2;
-   /*double t34;*/
+   strcpy(tmpout,preop);
-   int i,j,j1, nc, ii, jj;
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
-     for(i=1; i<= nlstate; i++){
+   return tmpout;
-       for(j=1; j<i;j++){
+ }
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-           /*s2 += param[i][j][nc]*cov[nc];*/
+ /*************** function subdirfext3 ***********/
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ char *subdirfext3(char fileres[], char *preop, char *postop)
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ {
-         }
-         ps[i][j]=s2;
+   /* Caution optionfilefiname is hidden */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+   strcpy(tmpout,optionfilefiname);
-       }
+   strcat(tmpout,"/");
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   strcat(tmpout,preop);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+   strcat(tmpout,fileres);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+   strcat(tmpout,postop);
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+   return tmpout;
-         }
+ }
-         ps[i][j]=s2;
-       }
+ char *asc_diff_time(long time_sec, char ascdiff[])
-     }
+ {
-     /*ps[3][2]=1;*/
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
-     for(i=1; i<= nlstate; i++){
+   sec_left = (time_sec) % (60*60*24);
-       s1=0;
+   hours = (sec_left) / (60*60) ;
-       for(j=1; j<i; j++)
+   sec_left = (sec_left) %(60*60);
-         s1+=exp(ps[i][j]);
+   minutes = (sec_left) /60;
-       for(j=i+1; j<=nlstate+ndeath; j++)
+   sec_left = (sec_left) % (60);
-         s1+=exp(ps[i][j]);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-       ps[i][i]=1./(s1+1.);
+   return ascdiff;
-       for(j=1; j<i; j++)
+ }
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ /***************** f1dim *************************/
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ extern int ncom;
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+ extern double *pcom,*xicom;
-     } /* end i */
+ extern double (*nrfunc)(double []);
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ double f1dim(double x)
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+ {
-         ps[ii][jj]=0;
+   int j;
-         ps[ii][ii]=1;
+   double f;
-       }
+   double *xt;
-     }
+   xt=vector(1,ncom);
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   f=(*nrfunc)(xt);
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   free_vector(xt,1,ncom);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+   return f;
- /*       } */
+ }
- /*       printf("\n "); */
- /*        } */
+ /*****************brent *************************/
- /*        printf("\n ");printf("%lf ",cov[2]); */
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-        /*
+ {
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       goto end;*/
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-     return ps;
+    * 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.
- /**************** Product of 2 matrices ******************/
+   */
+   int iter;
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+   double a,b,d,etemp;
- {
+   double fu=0,fv,fw,fx;
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+   double ftemp=0.;
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   /* in, b, out are matrice of pointers which should have been initialized
+   double e=0.0;
-      before: only the contents of out is modified. The function returns
-      a pointer to pointers identical to out */
+   a=(ax < cx ? ax : cx);
-   long i, j, k;
+   b=(ax > cx ? ax : cx);
-   for(i=nrl; i<= nrh; i++)
+   x=w=v=bx;
-     for(k=ncolol; k<=ncoloh; k++)
+   fw=fv=fx=(*f)(x);
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+   for (iter=1;iter<=ITMAX;iter++) {
-         out[i][k] +=in[i][j]*b[j][k];
+     xm=0.5*(a+b);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   return out;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
- }
+     printf(".");fflush(stdout);
+     fprintf(ficlog,".");fflush(ficlog);
+ #ifdef DEBUGBRENT
- /************* Higher Matrix Product ***************/
+     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- {
+ #endif
-   /* Computes the transition matrix starting at age 'age' over
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-      'nhstepm*hstepm*stepm' months (i.e. until
+       *xmin=x;
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       return fx;
-      nhstepm*hstepm matrices.
+     }
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     ftemp=fu;
-      (typically every 2 years instead of every month which is too big
+     if (fabs(e) > tol1) {
-      for the memory).
+       r=(x-w)*(fx-fv);
-      Model is determined by parameters x and covariates have to be
+       q=(x-v)*(fx-fw);
-      included manually here.
+       p=(x-v)*q-(x-w)*r;
+       q=2.0*(q-r);
-      */
+       if (q > 0.0) p = -p;
+       q=fabs(q);
-   int i, j, d, h, k;
+       etemp=e;
-   double **out, cov[NCOVMAX];
+       e=d;
-   double **newm;
+       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));
-   /* Hstepm could be zero and should return the unit matrix */
+       else {
-   for (i=1;i<=nlstate+ndeath;i++)
+                                 d=p/q;
-     for (j=1;j<=nlstate+ndeath;j++){
+                                 u=x+d;
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+                                 if (u-a < tol2 || b-u < tol2)
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+                                         d=SIGN(tol1,xm-x);
-     }
+       }
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+     } else {
-   for(h=1; h <=nhstepm; h++){
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     for(d=1; d <=hstepm; d++){
+     }
-       newm=savm;
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-       /* Covariates have to be included here again */
+     fu=(*f)(u);
-       cov[1]=1.;
+     if (fu <= fx) {
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       if (u >= x) a=x; else b=x;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       SHFT(v,w,x,u)
-       for (k=1; k<=cptcovage;k++)
+       SHFT(fv,fw,fx,fu)
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     } else {
-       for (k=1; k<=cptcovprod;k++)
+       if (u < x) a=u; else b=u;
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       if (fu <= fw || w == x) {
+                                 v=w;
+                                 w=u;
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+                                 fv=fw;
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+                                 fw=fu;
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+       } else if (fu <= fv || v == x || v == w) {
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+                                 v=u;
-       savm=oldm;
+                                 fv=fu;
-       oldm=newm;
+       }
      }
-     for(i=1; i<=nlstate+ndeath; i++)
+   }
-       for(j=1;j<=nlstate+ndeath;j++) {
+   nrerror("Too many iterations in brent");
-         po[i][j][h]=newm[i][j];
+   *xmin=x;
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   return fx;
-          */
+ }
-       }
-   } /* end h */
+ /****************** mnbrak ***********************/
-   return po;
- }
+ 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
- /*************** log-likelihood *************/
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
- double func( double *x)
+ 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.
-   int i, ii, j, k, mi, d, kk;
+    */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double ulim,u,r,q, dum;
-   double **out;
+   double fu;
-   double sw; /* Sum of weights */
-   double lli; /* Individual log likelihood */
+   double scale=10.;
-   int s1, s2;
+   int iterscale=0;
-   double bbh, survp;
-   long ipmx;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
-   /*extern weight */
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
-   /* We are differentiating ll according to initial status */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*for(i=1;i<imx;i++)
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
-     printf(" %d\n",s[4][i]);
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
-   */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-   cov[1]=1.;
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
+   /* } */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   if (*fb > *fa) {
-   if(mle==1){
+     SHFT(dum,*ax,*bx,dum)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     SHFT(dum,*fb,*fa,dum)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   }
-       for(mi=1; mi<= wav[i]-1; mi++){
+   *cx=(*bx)+GOLD*(*bx-*ax);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   *fc=(*func)(*cx);
-           for (j=1;j<=nlstate+ndeath;j++){
+ #ifdef DEBUG
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-           }
+ #endif
-         for(d=0; d<dh[mi][i]; d++){
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
-           newm=savm;
+     r=(*bx-*ax)*(*fb-*fc);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
-           for (kk=1; kk<=cptcovage;kk++) {
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       (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 abscissa where function should be evaluated */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       fu=(*func)(u);
-           savm=oldm;
+ #ifdef DEBUG
-           oldm=newm;
+       /* f(x)=A(x-u)**2+f(u) */
-         } /* end mult */
+       double A, fparabu;
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       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);
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+       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);
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-          * probability in order to take into account the bias as a fraction of the way
+ #endif
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+ #ifdef MNBRAKORIGINAL
-          * -stepm/2 to stepm/2 .
+ #else
-          * For stepm=1 the results are the same as for previous versions of Imach.
+ /*       if (fu > *fc) { */
-          * For stepm > 1 the results are less biased than in previous versions.
+ /* #ifdef DEBUG */
-          */
+ /*       printf("mnbrak4  fu > fc \n"); */
-         s1=s[mw[mi][i]][i];
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
-         s2=s[mw[mi+1][i]][i];
+ /* #endif */
-         bbh=(double)bh[mi][i]/(double)stepm;
+ /*      /\* 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 *\\/  *\/ */
-         /* bias bh is positive if real duration
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
-          * is higher than the multiple of stepm and negative otherwise.
+ /*      dum=u; /\* Shifting c and u *\/ */
-          */
+ /*      u = *cx; */
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+ /*      *cx = dum; */
-         if( s2 > nlstate){
+ /*      dum = fu; */
-           /* i.e. if s2 is a death state and if the date of death is known
+ /*      fu = *fc; */
-              then the contribution to the likelihood is the probability to
+ /*      *fc =dum; */
-              die between last step unit time and current  step unit time,
+ /*       } else { /\* end *\/ */
-              which is also equal to probability to die before dh
+ /* #ifdef DEBUG */
-              minus probability to die before dh-stepm .
+ /*       printf("mnbrak3  fu < fc \n"); */
-              In version up to 0.92 likelihood was computed
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-         as if date of death was unknown. Death was treated as any other
+ /* #endif */
-         health state: the date of the interview describes the actual state
+ /*      dum=u; /\* Shifting c and u *\/ */
-         and not the date of a change in health state. The former idea was
+ /*      u = *cx; */
-         to consider that at each interview the state was recorded
+ /*      *cx = dum; */
-         (healthy, disable or death) and IMaCh was corrected; but when we
+ /*      dum = fu; */
-         introduced the exact date of death then we should have modified
+ /*      fu = *fc; */
-         the contribution of an exact death to the likelihood. This new
+ /*      *fc =dum; */
-         contribution is smaller and very dependent of the step unit
+ /*       } */
-         stepm. It is no more the probability to die between last interview
+ #ifdef DEBUGMNBRAK
-         and month of death but the probability to survive from last
+                  double A, fparabu;
-         interview up to one month before death multiplied by the
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         probability to die within a month. Thanks to Chris
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
-         Jackson for correcting this bug.  Former versions increased
+      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);
-         mortality artificially. The bad side is that we add another loop
+      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);
-         which slows down the processing. The difference can be up to 10%
+ #endif
-         lower mortality.
+       dum=u; /* Shifting c and u */
-           */
+       u = *cx;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       *cx = dum;
+       dum = fu;
+       fu = *fc;
-         } else if  (s2==-2) {
+       *fc =dum;
-           for (j=1,survp=0. ; j<=nlstate; j++)
+ #endif
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-           /*survp += out[s1][j]; */
+ #ifdef DEBUG
-           lli= log(survp);
+       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
-         else if  (s2==-4) {
+       fu=(*func)(u);
-           for (j=3,survp=0. ; j<=nlstate; j++)
+       if (fu < *fc) {
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ #ifdef DEBUG
-           lli= log(survp);
+                                 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
-         else if  (s2==-5) {
+                           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-           for (j=1,survp=0. ; j<=2; j++)
+                                 SHFT(*fb,*fc,fu,(*func)(u))
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ #ifdef DEBUG
-           lli= log(survp);
+                                         printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
-         }
+ #endif
+       }
-         else{
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ #ifdef DEBUG
-           /*  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 */
+       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);
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+ #endif
-         /*if(lli ==000.0)*/
+       u=ulim;
-         /*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); */
+       fu=(*func)(u);
-         ipmx +=1;
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
-         sw += weight[i];
+ #ifdef DEBUG
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
-       } /* end of wave */
+       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);
-     } /* end of individual */
+ #endif
-   }  else if(mle==2){
+       u=(*cx)+GOLD*(*cx-*bx);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       fu=(*func)(u);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #ifdef DEBUG
-       for(mi=1; mi<= wav[i]-1; mi++){
+       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
-           for (j=1;j<=nlstate+ndeath;j++){
+ #endif
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     } /* end tests */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     SHFT(*ax,*bx,*cx,u)
-           }
+     SHFT(*fa,*fb,*fc,fu)
-         for(d=0; d<=dh[mi][i]; d++){
+ #ifdef DEBUG
-           newm=savm;
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-           for (kk=1; kk<=cptcovage;kk++) {
+ #endif
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-           }
+ }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ /*************** linmin ************************/
-           savm=oldm;
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-           oldm=newm;
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-         } /* end mult */
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
+ the value of func at the returned location p . This is actually all accomplished by calling the
-         s1=s[mw[mi][i]][i];
+ routines mnbrak and brent .*/
-         s2=s[mw[mi+1][i]][i];
+ int ncom;
-         bbh=(double)bh[mi][i]/(double)stepm;
+ double *pcom,*xicom;
-         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 */
+ double (*nrfunc)(double []);
-         ipmx +=1;
-         sw += weight[i];
+ #ifdef LINMINORIGINAL
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-       } /* end of wave */
+ #else
-     } /* end of individual */
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+ #endif
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ {
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   double brent(double ax, double bx, double cx,
-       for(mi=1; mi<= wav[i]-1; mi++){
+                double (*f)(double), double tol, double *xmin);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   double f1dim(double x);
-           for (j=1;j<=nlstate+ndeath;j++){
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+               double *fc, double (*func)(double));
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   int j;
-           }
+   double xx,xmin,bx,ax;
-         for(d=0; d<dh[mi][i]; d++){
+   double fx,fb,fa;
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #ifdef LINMINORIGINAL
-           for (kk=1; kk<=cptcovage;kk++) {
+ #else
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   double scale=10., axs, xxs; /* Scale added for infinity */
-           }
+ #endif
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   ncom=n;
-           savm=oldm;
+   pcom=vector(1,n);
-           oldm=newm;
+   xicom=vector(1,n);
-         } /* end mult */
+   nrfunc=func;
+   for (j=1;j<=n;j++) {
-         s1=s[mw[mi][i]][i];
+     pcom[j]=p[j];
-         s2=s[mw[mi+1][i]][i];
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
-         bbh=(double)bh[mi][i]/(double)stepm;
+   }
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         ipmx +=1;
+ #ifdef LINMINORIGINAL
-         sw += weight[i];
+   xx=1.;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ #else
-       } /* end of wave */
+   axs=0.0;
-     } /* end of individual */
+   xxs=1.;
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+   do{
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     xx= xxs;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #endif
-       for(mi=1; mi<= wav[i]-1; mi++){
+     ax=0.;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
-           for (j=1;j<=nlstate+ndeath;j++){
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* 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))   */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* 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) */
-         for(d=0; d<dh[mi][i]; d++){
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-           newm=savm;
+     /* 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]]*/
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #ifdef LINMINORIGINAL
-           for (kk=1; kk<=cptcovage;kk++) {
+ #else
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     if (fx != fx){
-           }
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+                         printf("|");
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+                         fprintf(ficlog,"|");
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef DEBUGLINMIN
-           savm=oldm;
+                         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);
-           oldm=newm;
+ #endif
-         } /* end mult */
+     }
+   }while(fx != fx && xxs > 1.e-5);
-         s1=s[mw[mi][i]][i];
+ #endif
-         s2=s[mw[mi+1][i]][i];
-         if( s2 > nlstate){
+ #ifdef DEBUGLINMIN
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   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);
-         }else{
+   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);
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ #endif
-         }
+ #ifdef LINMINORIGINAL
-         ipmx +=1;
+ #else
-         sw += weight[i];
+         if(fb == fx){ /* Flat function in the direction */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+                 xmin=xx;
- /*      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]); */
+     *flat=1;
-       } /* end of wave */
+         }else{
-     } /* end of individual */
+     *flat=0;
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+ #endif
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
-       for(mi=1; mi<= wav[i]-1; mi++){
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* fmin = f(p[j] + xmin * xi[j]) */
-           for (j=1;j<=nlstate+ndeath;j++){
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef DEBUG
-           }
+   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);
-         for(d=0; d<dh[mi][i]; d++){
+   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);
-           newm=savm;
+ #endif
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #ifdef LINMINORIGINAL
-           for (kk=1; kk<=cptcovage;kk++) {
+ #else
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+                         }
-           }
+ #endif
+ #ifdef DEBUGLINMIN
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   printf("linmin end ");
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   fprintf(ficlog,"linmin end ");
-           savm=oldm;
+ #endif
-           oldm=newm;
+   for (j=1;j<=n;j++) {
-         } /* end mult */
+ #ifdef LINMINORIGINAL
+     xi[j] *= xmin;
-         s1=s[mw[mi][i]][i];
+ #else
-         s2=s[mw[mi+1][i]][i];
+ #ifdef DEBUGLINMIN
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+     if(xxs <1.0)
-         ipmx +=1;
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
-         sw += weight[i];
+ #endif
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     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) */
-         /*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]);*/
+ #ifdef DEBUGLINMIN
-       } /* end of wave */
+     if(xxs <1.0)
-     } /* end of individual */
+       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 );
-   } /* End of if */
+ #endif
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ #endif
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   }
-   return -l;
+ #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));
- /*************** log-likelihood *************/
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
- double funcone( double *x)
+   for (j=1;j<=n;j++) {
- {
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-   /* Same as likeli but slower because of a lot of printf and if */
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-   int i, ii, j, k, mi, d, kk;
+     if(j % ncovmodel == 0){
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+       printf("\n");
-   double **out;
+       fprintf(ficlog,"\n");
-   double lli; /* Individual log likelihood */
+     }
-   double llt;
+   }
-   int s1, s2;
+ #else
-   double bbh, survp;
+ #endif
-   /*extern weight */
+   free_vector(xicom,1,n);
-   /* We are differentiating ll according to initial status */
+   free_vector(pcom,1,n);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ }
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
-   */
+ /*************** powell ************************/
-   cov[1]=1.;
+ /*
+ Minimization of a function func of n variables. Input consists of an initial starting point
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ 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
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-     for(mi=1; mi<= wav[i]-1; mi++){
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+  */
-         for (j=1;j<=nlstate+ndeath;j++){
+ #ifdef LINMINORIGINAL
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #else
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         int *flatdir; /* Function is vanishing in that direction */
-         }
+         int flat=0, flatd=0; /* Function is vanishing in that direction */
-       for(d=0; d<dh[mi][i]; d++){
+ #endif
-         newm=savm;
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+             double (*func)(double []))
-         for (kk=1; kk<=cptcovage;kk++) {
+ {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef LINMINORIGINAL
-         }
+  void linmin(double p[], double xi[], int n, double *fret,
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+               double (*func)(double []));
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #else
-         savm=oldm;
+  void linmin(double p[], double xi[], int n, double *fret,
-         oldm=newm;
+              double (*func)(double []),int *flat);
-       } /* end mult */
+ #endif
+  int i,ibig,j,jk,k;
-       s1=s[mw[mi][i]][i];
+   double del,t,*pt,*ptt,*xit;
-       s2=s[mw[mi+1][i]][i];
+   double directest;
-       bbh=(double)bh[mi][i]/(double)stepm;
+   double fp,fptt;
-       /* bias is positive if real duration
+   double *xits;
-        * is higher than the multiple of stepm and negative otherwise.
+   int niterf, itmp;
-        */
+ #ifdef LINMINORIGINAL
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+ #else
-         lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if  (s2==-2) {
+   flatdir=ivector(1,n);
-         for (j=1,survp=0. ; j<=nlstate; j++)
+   for (j=1;j<=n;j++) flatdir[j]=0;
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ #endif
-         lli= log(survp);
-       }else if (mle==1){
+   pt=vector(1,n);
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+   ptt=vector(1,n);
-       } else if(mle==2){
+   xit=vector(1,n);
-         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 */
+   xits=vector(1,n);
-       } else if(mle==3){  /* exponential inter-extrapolation */
+   *fret=(*func)(p);
-         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+   for (j=1;j<=n;j++) pt[j]=p[j];
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+   rcurr_time = time(NULL);
-         lli=log(out[s1][s2]); /* Original formula */
+   for (*iter=1;;++(*iter)) {
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+     fp=(*fret); /* From former iteration or initial value */
-         lli=log(out[s1][s2]); /* Original formula */
+     ibig=0;
-       } /* End of if */
+     del=0.0;
-       ipmx +=1;
+     rlast_time=rcurr_time;
-       sw += weight[i];
+     /* (void) gettimeofday(&curr_time,&tzp); */
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     rcurr_time = time(NULL);
- /*       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]); */
+     curr_time = *localtime(&rcurr_time);
-       if(globpr){
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-  %11.6f %11.6f %11.6f ", \
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+     for (i=1;i<=n;i++) {
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+       fprintf(ficrespow," %.12lf", p[i]);
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+     }
-           llt +=ll[k]*gipmx/gsw;
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+     printf("\n#model=  1      +     age ");
-         }
+     fprintf(ficlog,"\n#model=  1      +     age ");
-         fprintf(ficresilk," %10.6f\n", -llt);
+     if(nagesqr==1){
-       }
+         printf("  + age*age  ");
-     } /* end of wave */
+         fprintf(ficlog,"  + age*age  ");
-   } /* end of individual */
+     }
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+     for(j=1;j <=ncovmodel-2;j++){
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+       if(Typevar[j]==0) {
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         printf("  +      V%d  ",Tvar[j]);
-   if(globpr==0){ /* First time we count the contributions and weights */
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
-     gipmx=ipmx;
+       }else if(Typevar[j]==1) {
-     gsw=sw;
+         printf("  +    V%d*age ",Tvar[j]);
-   }
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
-   return -l;
+       }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]);
+       }
- /*************** function likelione ***********/
+     }
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+     printf("\n");
- {
+ /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
-   /* This routine should help understanding what is done with
+ /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
-      the selection of individuals/waves and
+     fprintf(ficlog,"\n");
-      to check the exact contribution to the likelihood.
+     for(i=1,jk=1; i <=nlstate; i++){
-      Plotting could be done.
+       for(k=1; k <=(nlstate+ndeath); k++){
-    */
+         if (k != i) {
-   int k;
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+           for(j=1; j <=ncovmodel; j++){
-     strcpy(fileresilk,"ilk");
+             printf("%12.7f ",p[jk]);
-     strcat(fileresilk,fileres);
+             fprintf(ficlog,"%12.7f ",p[jk]);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+             jk++;
-       printf("Problem with resultfile: %s\n", fileresilk);
+           }
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+           printf("\n");
-     }
+           fprintf(ficlog,"\n");
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+         }
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+       }
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+     }
-     for(k=1; k<=nlstate; k++)
+     if(*iter <=3 && *iter >1){
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+       tml = *localtime(&rcurr_time);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+       strcpy(strcurr,asctime(&tml));
-   }
+       rforecast_time=rcurr_time;
+       itmp = strlen(strcurr);
-   *fretone=(*funcone)(p);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-   if(*globpri !=0){
+         strcurr[itmp-1]='\0';
-     fclose(ficresilk);
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-     fflush(fichtm);
+       for(niterf=10;niterf<=30;niterf+=10){
-   }
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-   return;
+         forecast_time = *localtime(&rforecast_time);
- }
+         strcpy(strfor,asctime(&forecast_time));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
- /*********** Maximum Likelihood Estimation ***************/
+           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);
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         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);
- {
+       }
-   int i,j, iter;
+     }
-   double **xi;
+     for (i=1;i<=n;i++) { /* For each direction i */
-   double fret;
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-   double fretone; /* Only one call to likelihood */
+       fptt=(*fret);
-   /*  char filerespow[FILENAMELENGTH];*/
+ #ifdef DEBUG
-   xi=matrix(1,npar,1,npar);
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-   for (i=1;i<=npar;i++)
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-     for (j=1;j<=npar;j++)
+ #endif
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-   strcpy(filerespow,"pow");
+ #ifdef LINMINORIGINAL
-   strcat(filerespow,fileres);
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ #else
-     printf("Problem with resultfile: %s\n", filerespow);
+       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+                         flatdir[i]=flat; /* Function is vanishing in that direction i */
-   }
+ #endif
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+                         /* Outputs are fret(new point p) p is updated and xit rescaled */
-   for (i=1;i<=nlstate;i++)
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-     for(j=1;j<=nlstate+ndeath;j++)
+                                 /* because that direction will be replaced unless the gain del is small */
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-   fprintf(ficrespow,"\n");
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
+                                 /* with the new direction. */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+                                 del=fabs(fptt-(*fret));
+                                 ibig=i;
-   free_matrix(xi,1,npar,1,npar);
+       }
-   fclose(ficrespow);
+ #ifdef DEBUG
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+       printf("%d %.12e",i,(*fret));
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       for (j=1;j<=n;j++) {
+                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
- }
+                                 printf(" x(%d)=%.12e",j,xit[j]);
+                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
- /**** Computes Hessian and covariance matrix ***/
+       }
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+       for(j=1;j<=n;j++) {
- {
+                                 printf(" p(%d)=%.12e",j,p[j]);
-   double  **a,**y,*x,pd;
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-   double **hess;
+       }
-   int i, j,jk;
+       printf("\n");
-   int *indx;
+       fprintf(ficlog,"\n");
+ #endif
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+     } /* end loop on each direction i */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+     /* New value of last point Pn is not computed, P(n-1) */
-   double gompertz(double p[]);
+       for(j=1;j<=n;j++) {
-   hess=matrix(1,npar,1,npar);
+                                 if(flatdir[j] >0){
+                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+                                 }
-   for (i=1;i<=npar;i++){
+                                 /* printf("\n"); */
-     printf("%d",i);fflush(stdout);
+                                 /* fprintf(ficlog,"\n"); */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+                         }
+     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+     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 */
-     /*  printf(" %f ",p[i]);
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+       /* 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) */
-   for (i=1;i<=npar;i++) {
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
-     for (j=1;j<=npar;j++)  {
+       /* By adding 10 parameters more the gain should be 18.31 */
-       if (j>i) {
-         printf(".%d%d",i,j);fflush(stdout);
+       /* Starting the program with initial values given by a former maximization will simply change */
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       /* 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.  */
-         hess[j][i]=hess[i][j];
+ #ifdef DEBUG
-         /*printf(" %lf ",hess[i][j]);*/
+       int k[2],l;
-       }
+       k[0]=1;
-     }
+       k[1]=-1;
-   }
+       printf("Max: %.12e",(*func)(p));
-   printf("\n");
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-   fprintf(ficlog,"\n");
+       for (j=1;j<=n;j++) {
+         printf(" %.12e",p[j]);
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+         fprintf(ficlog," %.12e",p[j]);
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+       }
+       printf("\n");
-   a=matrix(1,npar,1,npar);
+       fprintf(ficlog,"\n");
-   y=matrix(1,npar,1,npar);
+       for(l=0;l<=1;l++) {
-   x=vector(1,npar);
+         for (j=1;j<=n;j++) {
-   indx=ivector(1,npar);
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-   for (i=1;i<=npar;i++)
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   ludcmp(a,npar,indx,&pd);
+         }
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   for (j=1;j<=npar;j++) {
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-     for (i=1;i<=npar;i++) x[i]=0;
+       }
-     x[j]=1;
+ #endif
-     lubksb(a,npar,indx,x);
-     for (i=1;i<=npar;i++){
+ #ifdef LINMINORIGINAL
-       matcov[i][j]=x[i];
+ #else
-     }
+       free_ivector(flatdir,1,n);
-   }
+ #endif
+       free_vector(xit,1,n);
-   printf("\n#Hessian matrix#\n");
+       free_vector(xits,1,n);
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+       free_vector(ptt,1,n);
-   for (i=1;i<=npar;i++) {
+       free_vector(pt,1,n);
-     for (j=1;j<=npar;j++) {
+       return;
-       printf("%.3e ",hess[i][j]);
+     } /* enough precision */
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
-     }
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-     printf("\n");
+       ptt[j]=2.0*p[j]-pt[j];
-     fprintf(ficlog,"\n");
+       xit[j]=p[j]-pt[j];
-   }
+       pt[j]=p[j];
+     }
-   /* Recompute Inverse */
+     fptt=(*func)(ptt); /* f_3 */
-   for (i=1;i<=npar;i++)
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+                 if (*iter <=4) {
-   ludcmp(a,npar,indx,&pd);
+ #else
+ #endif
-   /*  printf("\n#Hessian matrix recomputed#\n");
+ #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
+ #else
-   for (j=1;j<=npar;j++) {
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-     for (i=1;i<=npar;i++) x[i]=0;
+ #endif
-     x[j]=1;
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-     lubksb(a,npar,indx,x);
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-     for (i=1;i<=npar;i++){
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-       y[i][j]=x[i];
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-       printf("%.3e ",y[i][j]);
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-       fprintf(ficlog,"%.3e ",y[i][j]);
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
-     }
+       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
-     printf("\n");
+       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
-     fprintf(ficlog,"\n");
+       /* 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 */
-   */
+       /* mu² and del² are equal when f3=f1 */
+                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
-   free_matrix(a,1,npar,1,npar);
+                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
-   free_matrix(y,1,npar,1,npar);
+                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
-   free_vector(x,1,npar);
+                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
-   free_ivector(indx,1,npar);
+ #ifdef NRCORIGINAL
-   free_matrix(hess,1,npar,1,npar);
+       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);
+ #endif
- /*************** hessian matrix ****************/
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+ #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);
-   int i;
+       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);
-   int l=1, lmax=20;
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   double k1,k2;
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-   double p2[NPARMAX+1];
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   double res;
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+       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);
-   double fx;
+       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);
-   int k=0,kmax=10;
+ #endif
-   double l1;
+ #ifdef POWELLORIGINAL
+       if (t < 0.0) { /* Then we use it for new direction */
-   fx=func(x);
+ #else
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-   for(l=0 ; l <=lmax; l++){
+                                 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);
-     l1=pow(10,l);
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-     delts=delt;
+         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);
-     for(k=1 ; k <kmax; k=k+1){
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-       delt = delta*(l1*k);
+       }
-       p2[theta]=x[theta] +delt;
+       if (directest < 0.0) { /* Then we use it for new direction */
-       k1=func(p2)-fx;
+ #endif
-       p2[theta]=x[theta]-delt;
+ #ifdef DEBUGLINMIN
-       k2=func(p2)-fx;
+         printf("Before linmin in direction P%d-P0\n",n);
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         for (j=1;j<=n;j++) {
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+           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]);
- #ifdef DEBUG
+           if(j % ncovmodel == 0){
-       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);
+             printf("\n");
-       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);
+             fprintf(ficlog,"\n");
- #endif
+           }
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+         }
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+ #endif
-         k=kmax;
+ #ifdef LINMINORIGINAL
-       }
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+ #else
-         k=kmax; l=lmax*10.;
+         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 */
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+ #endif
-         delts=delt;
-       }
+ #ifdef DEBUGLINMIN
-     }
+         for (j=1;j<=n;j++) {
-   }
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-   delti[theta]=delts;
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-   return res;
+           if(j % ncovmodel == 0){
+             printf("\n");
- }
+             fprintf(ficlog,"\n");
+           }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+         }
- {
+ #endif
-   int i;
+         for (j=1;j<=n;j++) {
-   int l=1, l1, lmax=20;
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-   double k1,k2,k3,k4,res,fx;
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-   double p2[NPARMAX+1];
+         }
-   int k;
+ #ifdef LINMINORIGINAL
+ #else
-   fx=func(x);
+         for (j=1, flatd=0;j<=n;j++) {
-   for (k=1; k<=2; k++) {
+           if(flatdir[j]>0)
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+             flatd++;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         }
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         if(flatd >0){
-     k1=func(p2)-fx;
+           printf("%d flat directions: ",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+           for (j=1;j<=n;j++) {
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+             if(flatdir[j]>0){
-     k2=func(p2)-fx;
+               printf("%d ",j);
+               fprintf(ficlog,"%d ",j);
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+             }
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+           }
-     k3=func(p2)-fx;
+           printf("\n");
+           fprintf(ficlog,"\n");
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         }
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ #endif
-     k4=func(p2)-fx;
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
- #ifdef DEBUG
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ #ifdef DEBUG
-     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);
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
- #endif
+         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++){
-   return res;
+           printf(" %lf",xit[j]);
- }
+           fprintf(ficlog," %lf",xit[j]);
+         }
- /************** Inverse of matrix **************/
+         printf("\n");
- void ludcmp(double **a, int n, int *indx, double *d)
+         fprintf(ficlog,"\n");
- {
+ #endif
-   int i,imax,j,k;
+       } /* end of t or directest negative */
-   double big,dum,sum,temp;
+ #ifdef POWELLNOF3INFF1TEST
-   double *vv;
+ #else
+       } /* end if (fptt < fp)  */
-   vv=vector(1,n);
+ #endif
-   *d=1.0;
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-   for (i=1;i<=n;i++) {
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
-     big=0.0;
+ #else
-     for (j=1;j<=n;j++)
+ #endif
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+                 } /* loop iteration */
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+ }
-     vv[i]=1.0/big;
-   }
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   for (j=1;j<=n;j++) {
-     for (i=1;i<j;i++) {
+   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
-       sum=a[i][j];
+   {
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
-       a[i][j]=sum;
+      *   (and selected quantitative values in nres)
-     }
+      *  by left multiplying the unit
-     big=0.0;
+      *  matrix by transitions matrix until convergence is reached with precision ftolpl
-     for (i=j;i<=n;i++) {
+      * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
-       sum=a[i][j];
+      * Wx is row vector: population in state 1, population in state 2, population dead
-       for (k=1;k<j;k++)
+      * or prevalence in state 1, prevalence in state 2, 0
-         sum -= a[i][k]*a[k][j];
+      * newm is the matrix after multiplications, its rows are identical at a factor.
-       a[i][j]=sum;
+      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+      * Output is prlim.
-         big=dum;
+      * Initial matrix pimij
-         imax=i;
+      */
-       }
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-     }
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-     if (j != imax) {
+   /*  0,                   0                  , 1} */
-       for (k=1;k<=n;k++) {
+   /*
-         dum=a[imax][k];
+    * and after some iteration: */
-         a[imax][k]=a[j][k];
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-         a[j][k]=dum;
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-       }
+   /*  0,                   0                  , 1} */
-       *d = -(*d);
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-       vv[imax]=vv[j];
+   /* {0.51571254859325999, 0.4842874514067399, */
-     }
+   /*  0.51326036147820708, 0.48673963852179264} */
-     indx[j]=imax;
+   /* If we start from prlim again, prlim tends to a constant matrix */
-     if (a[j][j] == 0.0) a[j][j]=TINY;
-     if (j != n) {
+   int i, ii,j,k;
-       dum=1.0/(a[j][j]);
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   /* double **matprod2(); */ /* test */
-     }
+   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
-   }
+   double **newm;
-   free_vector(vv,1,n);  /* Doesn't work */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
- ;
+   int ncvloop=0;
- }
+   int first=0;
- void lubksb(double **a, int n, int *indx, double b[])
+   min=vector(1,nlstate);
- {
+   max=vector(1,nlstate);
-   int i,ii=0,ip,j;
+   meandiff=vector(1,nlstate);
-   double sum;
+         /* Starting with matrix unity */
-   for (i=1;i<=n;i++) {
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-     ip=indx[i];
+     for (j=1;j<=nlstate+ndeath;j++){
-     sum=b[ip];
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     b[ip]=b[i];
+     }
-     if (ii)
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+   cov[1]=1.;
-     else if (sum) ii=i;
-     b[i]=sum;
+   /* 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 (i=n;i>=1;i--) {
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-     sum=b[i];
+     ncvloop++;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     newm=savm;
-     b[i]=sum/a[i][i];
+     /* Covariates have to be included here again */
-   }
+     cov[2]=agefin;
- }
+     if(nagesqr==1)
+       cov[3]= agefin*agefin;;
- void pstamp(FILE *fichier)
+     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 */
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+       cov[2+nagesqr+TvarsDind[k]]=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)); */
+     }
- /************ Frequencies ********************/
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
- 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[])
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
- {  /* Some frequencies */
+       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]); */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+     }
-   int first;
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
-   double ***freq; /* Frequencies */
+       if(Dummy[Tvar[Tage[k]]]){
-   double *pp, **prop;
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+       } else{
-   char fileresp[FILENAMELENGTH];
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       }
-   pp=vector(1,nlstate);
+       /* 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]); */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     }
-   strcpy(fileresp,"p");
+     for (k=1; k<=cptcovprod;k++){ /* For product without age */
-   strcat(fileresp,fileres);
+       /* 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((ficresp=fopen(fileresp,"w"))==NULL) {
+       if(Dummy[Tvard[k][1]==0]){
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+         if(Dummy[Tvard[k][2]==0]){
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-     exit(0);
+         }else{
-   }
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+         }
-   j1=0;
+       }else{
+         if(Dummy[Tvard[k][2]==0]){
-   j=cptcoveff;
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         }else{
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
-   first=1;
+         }
+       }
-   for(k1=1; k1<=j;k1++){
+     }
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       j1++;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-         scanf("%d", i);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-       for (i=-5; i<=nlstate+ndeath; i++)
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+                 /* age and covariate values of ij are in 'cov' */
-           for(m=iagemin; m <= iagemax+3; m++)
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-             freq[i][jk][m]=0;
+     savm=oldm;
-     for (i=1; i<=nlstate; i++)
+     oldm=newm;
-       for(m=iagemin; m <= iagemax+3; m++)
-         prop[i][m]=0;
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
-       dateintsum=0;
+       min[j]=1.;
-       k2cpt=0;
+     }
-       for (i=1; i<=imx; i++) {
+     for(i=1;i<=nlstate;i++){
-         bool=1;
+       sumnew=0;
-         if  (cptcovn>0) {
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-           for (z1=1; z1<=cptcoveff; z1++)
+       for(j=1; j<=nlstate; j++){
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-               bool=0;
+         max[j]=FMAX(max[j],prlim[i][j]);
-         }
+         min[j]=FMIN(min[j],prlim[i][j]);
-         if (bool==1){
+       }
-           for(m=firstpass; m<=lastpass; m++){
+     }
-             k2=anint[m][i]+(mint[m][i]/12.);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+     maxmax=0.;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     for(j=1; j<=nlstate; j++){
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+       maxmax=FMAX(maxmax,meandiff[j]);
-               if (m<lastpass) {
+       /* 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); */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     } /* j loop */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+     *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){
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-                 dateintsum=dateintsum+k2;
+       free_vector(min,1,nlstate);
-                 k2cpt++;
+       free_vector(max,1,nlstate);
-               }
+       free_vector(meandiff,1,nlstate);
-               /*}*/
+       return prlim;
-           }
+     }
-         }
+   } /* agefin loop */
-       }
+     /* After some age loop it doesn't converge */
+   if(!first){
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     first=1;
-       pstamp(ficresp);
+     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);
-       if  (cptcovn>0) {
+   }
-         fprintf(ficresp, "\n#********** Variable ");
+   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);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresp, "**********\n#");
+   /* 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);
-       for(i=1; i<=nlstate;i++)
+   free_vector(max,1,nlstate);
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   free_vector(meandiff,1,nlstate);
-       fprintf(ficresp, "\n");
+   return prlim; /* should not reach here */
-       for(i=iagemin; i <= iagemax+3; i++){
+ }
-         if(i==iagemax+3){
-           fprintf(ficlog,"Total");
-         }else{
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
-           if(first==1){
-             first=0;
+  /* 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) */
-             printf("See log file for details...\n");
+  /* 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) */
-           }
+   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
-           fprintf(ficlog,"Age %d", i);
+ {
-         }
+   /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
-         for(jk=1; jk <=nlstate ; jk++){
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-             pp[jk] += freq[jk][m][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 */
-         for(jk=1; jk <=nlstate ; jk++){
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-           for(m=-1, pos=0; m <=0 ; m++)
+   /* Initial matrix pimij */
-             pos += freq[jk][m][i];
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-           if(pp[jk]>=1.e-10){
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-             if(first==1){
+   /*  0,                   0                  , 1} */
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   /*
-             }
+    * and after some iteration: */
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-           }else{
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-             if(first==1)
+   /*  0,                   0                  , 1} */
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   /* {0.51571254859325999, 0.4842874514067399, */
-           }
+   /*  0.51326036147820708, 0.48673963852179264} */
-         }
+   /* If we start from prlim again, prlim tends to a constant matrix */
-         for(jk=1; jk <=nlstate ; jk++){
+   int i, ii,j,k;
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+   int first=0;
-             pp[jk] += freq[jk][m][i];
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-         }
+   /* double **matprod2(); */ /* test */
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+   double **out, cov[NCOVMAX+1], **bmij();
-           pos += pp[jk];
+   double **newm;
-           posprop += prop[jk][i];
+   double         **dnewm, **doldm, **dsavm;  /* for use */
-         }
+   double         **oldm, **savm;  /* for use */
-         for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-             if(first==1)
+   int ncvloop=0;
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   min=vector(1,nlstate);
-           }else{
+   max=vector(1,nlstate);
-             if(first==1)
+   meandiff=vector(1,nlstate);
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
-           }
+   oldm=oldms; savm=savms;
-           if( i <= iagemax){
-             if(pos>=1.e-5){
+   /* Starting with matrix unity */
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+     for (j=1;j<=nlstate+ndeath;j++){
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             }
+     }
-             else
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   cov[1]=1.;
-           }
-         }
+   /* 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(jk=-1; jk <=nlstate+ndeath; jk++)
+   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-           for(m=-1; m <=nlstate+ndeath; m++)
+   /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-             if(freq[jk][m][i] !=0 ) {
+   for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
-             if(first==1)
+     ncvloop++;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
-             }
+     /* Covariates have to be included here again */
-         if(i <= iagemax)
+     cov[2]=agefin;
-           fprintf(ficresp,"\n");
+     if(nagesqr==1)
-         if(first==1)
+       cov[3]= agefin*agefin;;
-           printf("Others in log...\n");
+     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-         fprintf(ficlog,"\n");
+                         /* 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,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)); */
-   }
+     }
-   dateintmean=dateintsum/k2cpt;
+     /* for (k=1; k<=cptcovn;k++) { */
+     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
-   fclose(ficresp);
+     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+     /*   /\* 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])]); *\/ */
-   free_vector(pp,1,nlstate);
+     /* } */
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-   /* End of Freq */
+                         /* 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]); */
- /************ Prevalence ********************/
+     }
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+     /* 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 *\/ */
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
-      We still use firstpass and lastpass as another selection.
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
-   */
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+       } else{
-   double ***freq; /* Frequencies */
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
-   double *pp, **prop;
+       }
-   double pos,posprop;
+       /* 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]); */
-   double  y2; /* in fractional years */
+     }
-   int iagemin, iagemax;
+     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]); */
-   iagemin= (int) agemin;
+       if(Dummy[Tvard[k][1]==0]){
-   iagemax= (int) agemax;
+         if(Dummy[Tvard[k][2]==0]){
-   /*pp=vector(1,nlstate);*/
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         }else{
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
-   j1=0;
+         }
+       }else{
-   j=cptcoveff;
+         if(Dummy[Tvard[k][2]==0]){
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
+         }else{
-   for(k1=1; k1<=j;k1++){
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
-     for(i1=1; i1<=ncodemax[k1];i1++){
+         }
-       j1++;
+       }
+     }
-       for (i=1; i<=nlstate; i++)
-         for(m=iagemin; m <= iagemax+3; m++)
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-           prop[i][m]=0.0;
+     /*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]);*/
-       for (i=1; i<=imx; i++) { /* Each individual */
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         bool=1;
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-         if  (cptcovn>0) {
+                 /* ij should be linked to the correct index of cov */
-           for (z1=1; z1<=cptcoveff; z1++)
+                 /* age and covariate values ij are in 'cov', but we need to pass
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+                  * ij for the observed prevalence at age and status and covariate
-               bool=0;
+                  * number:  prevacurrent[(int)agefin][ii][ij]
-         }
+                  */
-         if (bool==1) {
+     /* 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 *\/ */
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+     /* 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 *\/ */
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+     /* if((int)age == 86 || (int)age == 87){ */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     /*   for(i=1; i<=nlstate+ndeath; i++) { */
-               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);
+     /*  printf("%d newm= ",i); */
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
-                 /*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]]);*/
+     /*    printf("%f ",newm[i][j]); */
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     /*  } */
-                 prop[s[m][i]][iagemax+3] += weight[i];
+     /*  printf("oldm * "); */
-               }
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
-             }
+     /*    printf("%f ",oldm[i][j]); */
-           } /* end selection of waves */
+     /*  } */
-         }
+     /*  printf(" bmmij "); */
-       }
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
-       for(i=iagemin; i <= iagemax+3; i++){
+     /*    printf("%f ",pmmij[i][j]); */
+     /*  } */
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     /*  printf("\n"); */
-           posprop += prop[jk][i];
+     /*   } */
-         }
+     /* } */
+     savm=oldm;
-         for(jk=1; jk <=nlstate ; jk++){
+     oldm=newm;
-           if( i <=  iagemax){
-             if(posprop>=1.e-5){
+     for(j=1; j<=nlstate; j++){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+       max[j]=0.;
-             }
+       min[j]=1.;
-           }
+     }
-         }/* end jk */
+     for(j=1; j<=nlstate; j++){
-       }/* end i */
+       for(i=1;i<=nlstate;i++){
-     } /* end i1 */
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
-   } /* end k1 */
+         bprlim[i][j]= newm[i][j];
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+         min[i]=FMIN(min[i],bprlim[i][j]);
-   /*free_vector(pp,1,nlstate);*/
+       }
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+     }
- }  /* End of prevalence */
+     maxmax=0.;
- /************* Waves Concatenation ***************/
+     for(i=1; i<=nlstate; i++){
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
- 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)
+       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); */
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+     } /* i loop */
-      Death is a valid wave (if date is known).
+     *ncvyear= -( (int)age- (int)agefin);
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+     if(maxmax < ftolpl){
-      and mw[mi+1][i]. dh depends on stepm.
+       /* 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);
-   int i, mi, m;
+       free_vector(meandiff,1,nlstate);
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+       return bprlim;
-      double sum=0., jmean=0.;*/
+     }
-   int first;
+   } /* agefin loop */
-   int j, k=0,jk, ju, jl;
+     /* After some age loop it doesn't converge */
-   double sum=0.;
+   if(!first){
-   first=0;
+     first=1;
-   jmin=1e+5;
+     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\
-   jmax=-1;
+ 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);
-   jmean=0.;
+   }
-   for(i=1; i<=imx; i++){
+   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\
-     mi=0;
+ 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);
-     m=firstpass;
+   /* 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); */
-     while(s[m][i] <= nlstate){
+   free_vector(min,1,nlstate);
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+   free_vector(max,1,nlstate);
-         mw[++mi][i]=m;
+   free_vector(meandiff,1,nlstate);
-       if(m >=lastpass)
-         break;
+   return bprlim; /* should not reach here */
-       else
+ }
-         m++;
-     }/* end while */
+ /*************** transition probabilities ***************/
-     if (s[m][i] > nlstate){
-       mi++;     /* Death is another wave */
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-       /* if(mi==0)  never been interviewed correctly before death */
+ {
-          /* Only death is a correct wave */
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-       mw[mi][i]=m;
+      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]
-     wav[i]=mi;
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-     if(mi==0){
+      ncth covariate in the global vector x is given by the formula:
-       nbwarn++;
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-       if(first==0){
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         first=1;
+      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
-       if(first==1){
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+      Sum on j ps[i][j] should equal to 1.
-       }
+   */
-     } /* end mi==0 */
+   double s1, lnpijopii;
-   } /* End individuals */
+   /*double t34;*/
+   int i,j, nc, ii, jj;
-   for(i=1; i<=imx; i++){
-     for(mi=1; mi<wav[i];mi++){
+   for(i=1; i<= nlstate; i++){
-       if (stepm <=0)
+     for(j=1; j<i;j++){
-         dh[mi][i]=1;
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-       else{
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-           if (agedc[i] < 2*AGESUP) {
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+       }
-             if(j==0) j=1;  /* Survives at least one month after exam */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-             else if(j<0){
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-               nberr++;
+     }
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+     for(j=i+1; j<=nlstate+ndeath;j++){
-               j=1; /* Temporary Dangerous patch */
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-             }
+       }
-             k=k+1;
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-             if (j >= jmax){
+     }
-               jmax=j;
+   }
-               ijmax=i;
-             }
+   for(i=1; i<= nlstate; i++){
-             if (j <= jmin){
+     s1=0;
-               jmin=j;
+     for(j=1; j<i; j++){
-               ijmin=i;
+       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); */
-             sum=sum+j;
+     }
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+     for(j=i+1; j<=nlstate+ndeath; j++){
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+       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); */
-         }
+     }
-         else{
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+     ps[i][i]=1./(s1+1.);
- /*        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]); */
+     /* Computing other pijs */
+     for(j=1; j<i; j++)
-           k=k+1;
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-           if (j >= jmax) {
+     for(j=i+1; j<=nlstate+ndeath; j++)
-             jmax=j;
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-             ijmax=i;
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-           }
+   } /* end i */
-           else if (j <= jmin){
-             jmin=j;
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-             ijmin=i;
+     for(jj=1; jj<= nlstate+ndeath; jj++){
-           }
+       ps[ii][jj]=0;
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+       ps[ii][ii]=1;
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+     }
-           if(j<0){
+   }
-             nberr++;
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-           }
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-           sum=sum+j;
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         }
+   /*   } */
-         jk= j/stepm;
+   /*   printf("\n "); */
-         jl= j -jk*stepm;
+   /* } */
-         ju= j -(jk+1)*stepm;
+   /* printf("\n ");printf("%lf ",cov[2]);*/
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   /*
-           if(jl==0){
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
-             dh[mi][i]=jk;
+                 goto end;*/
-             bh[mi][i]=0;
+   return ps; /* Pointer is unchanged since its call */
-           }else{ /* We want a negative bias in order to only have interpolation ie
+ }
-                   * at the price of an extra matrix product in likelihood */
-             dh[mi][i]=jk+1;
+ /*************** backward transition probabilities ***************/
-             bh[mi][i]=ju;
-           }
+  /* 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 ) */
-         }else{
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-           if(jl <= -ju){
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
-             dh[mi][i]=jk;
+ {
-             bh[mi][i]=jl;       /* bias is positive if real duration
+   /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
-                                  * is higher than the multiple of stepm and negative otherwise.
+    * 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;
-           else{
-             dh[mi][i]=jk+1;
+   double **out, **pmij();
-             bh[mi][i]=ju;
+   double sumnew=0.;
-           }
+   double agefin;
-           if(dh[mi][i]==0){
+   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
-             dh[mi][i]=1; /* At least one step */
+   double **dnewm, **dsavm, **doldm;
-             bh[mi][i]=ju; /* At least one step */
+   double **bbmij;
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-           }
+   doldm=ddoldms; /* global pointers */
-         } /* end if mle */
+   dnewm=ddnewms;
-       }
+   dsavm=ddsavms;
-     } /* end wave */
-   }
+   agefin=cov[2];
-   jmean=sum/k;
+   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
-   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);
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+      the observed prevalence (with this covariate ij) at beginning of transition */
-  }
+   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
- /*********** Tricode ****************************/
+   /* P_x */
- void tricode(int *Tvar, int **nbcode, int imx)
+   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
- {
+   /* outputs pmmij which is a stochastic matrix in row */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   /* Diag(w_x) */
-   int cptcode=0;
+   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
-   cptcoveff=0;
+   sumnew=0.;
+   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+     /* 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];
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   }
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   if(sumnew >0.01){  /* At least some value in the prevalence */
-                                modality*/
+     for (ii=1;ii<=nlstate+ndeath;ii++){
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       for (j=1;j<=nlstate+ndeath;j++)
-       Ndum[ij]++; /*store the modality */
+         doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+     }
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+   }else{
-                                        Tvar[j]. If V=sex and male is 0 and
+     for (ii=1;ii<=nlstate+ndeath;ii++){
-                                        female is 1, then  cptcode=1.*/
+       for (j=1;j<=nlstate+ndeath;j++)
-     }
+       doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
+     }
-     for (i=0; i<=cptcode; i++) {
+     /* if(sumnew <0.9){ */
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
-     }
+     /* } */
+   }
-     ij=1;
+   k3=0.0;  /* We put the last diagonal to 0 */
-     for (i=1; i<=ncodemax[j]; i++) {
+   for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
-       for (k=0; k<= maxncov; k++) {
+       doldm[ii][ii]= k3;
-         if (Ndum[k] != 0) {
+   }
-           nbcode[Tvar[j]][ij]=k;
+   /* End doldm, At the end doldm is diag[(w_i)] */
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+   /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
-           ij++;
+   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
-         }
-         if (ij > ncodemax[j]) break;
+   /* 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++){
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
+       sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
-  for (i=1; i<=ncovmodel-2; i++) {
+     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+     for (ii=1;ii<=nlstate+ndeath;ii++){
-    ij=Tvar[i];
+         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
-    Ndum[ij]++;
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
-  }
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
-  ij=1;
+         /* }else */
-  for (i=1; i<= maxncov; i++) {
+       dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+     } /*End ii */
-      Tvaraff[ij]=i; /*For printing */
+   } /* 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 */
-      ij++;
-    }
+   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 */
-  cptcoveff=ij-1; /*Number of simple covariates*/
+   return ps; /*pointer is unchanged */
  }
+ /*************** transition probabilities ***************/
- /*********** Health Expectancies ****************/
+ double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+ {
+   /* 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
-   /* Health expectancies, no variances */
+      model to the ncovmodel covariates (including constant and age).
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-   double age, agelim, hf;
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-   double ***p3mat;
+      ncth covariate in the global vector x is given by the formula:
-   double eip;
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-   pstamp(ficreseij);
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-   fprintf(ficreseij,"# Age");
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-   for(i=1; i<=nlstate;i++){
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-     for(j=1; j<=nlstate;j++){
+   */
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   double s1, lnpijopii;
-     }
+   /*double t34;*/
-     fprintf(ficreseij," e%1d. ",i);
+   int i,j, nc, ii, jj;
-   }
-   fprintf(ficreseij,"\n");
+   for(i=1; i<= nlstate; i++){
+     for(j=1; j<i;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   if(estepm < stepm){
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-   }
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   else  hstepm=estepm;
+       }
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-    * This is mainly to measure the difference between two models: for example
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+     }
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+     for(j=i+1; j<=nlstate+ndeath;j++){
-    * progression in between and thus overestimating or underestimating according
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-    * to the curvature of the survival function. If, for the same date, we
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-    * to compare the new estimate of Life expectancy with the same linear
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-    * hypothesis. A more precise result, taking into account a more precise
+       }
-    * curvature will be obtained if estepm is as small as stepm. */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+     }
-   /* 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
+   for(i=1; i<= nlstate; i++){
-      nstepm is the number of stepm from age to agelin.
+     s1=0;
-      Look at hpijx to understand the reason of that which relies in memory size
+     for(j=1; j<i; j++){
-      and note for a fixed period like estepm months */
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-      survival function given by stepm (the optimization length). Unfortunately it
+     }
-      means that if the survival funtion is printed only each two years of age and if
+     for(j=i+1; j<=nlstate+ndeath; j++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-      results. So we changed our mind and took the option of the best precision.
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   */
+     }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     ps[i][i]=1./(s1+1.);
-   agelim=AGESUP;
+     /* Computing other pijs */
-   /* If stepm=6 months */
+     for(j=1; j<i; j++)
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     for(j=i+1; j<=nlstate+ndeath; j++)
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
- /* nhstepm age range expressed in number of stepm */
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   } /* end i */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   /* if (stepm >= YEARM) hstepm=1;*/
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     for(jj=1; jj<= nlstate+ndeath; jj++){
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       ps[ii][jj]=0;
+       ps[ii][ii]=1;
-   for (age=bage; age<=fage; age ++){
+     }
+   }
+   /* Added for backcast */ /* Transposed matrix too */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     s1=0.;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     for(ii=1; ii<= nlstate+ndeath; ii++){
+       s1+=ps[ii][jj];
-     printf("%d|",(int)age);fflush(stdout);
+     }
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     for(ii=1; ii<= nlstate; ii++){
+       ps[ii][jj]=ps[ii][jj]/s1;
+     }
-     /* Computing expectancies */
+   }
-     for(i=1; i<=nlstate;i++)
+   /* Transposition */
-       for(j=1; j<=nlstate;j++)
+   for(jj=1; jj<= nlstate+ndeath; jj++){
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+       s1=ps[ii][jj];
+       ps[ii][jj]=ps[jj][ii];
-           /*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]);*/
+       ps[jj][ii]=s1;
+     }
-         }
+   }
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     fprintf(ficreseij,"%3.0f",age );
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-     for(i=1; i<=nlstate;i++){
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-       eip=0;
+   /*   } */
-       for(j=1; j<=nlstate;j++){
+   /*   printf("\n "); */
-         eip +=eij[i][j][(int)age];
+   /* } */
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+   /* printf("\n ");printf("%lf ",cov[2]);*/
-       }
+   /*
-       fprintf(ficreseij,"%9.4f", eip );
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
-     }
+     goto end;*/
-     fprintf(ficreseij,"\n");
+   return ps;
+ }
-   }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   printf("\n");
+ /**************** Product of 2 matrices ******************/
-   fprintf(ficlog,"\n");
+ 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
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+      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
-   /* Covariances of health expectancies eij and of total life expectancies according
+      a pointer to pointers identical to out */
-    to initial status i, ei. .
+   int i, j, k;
-   */
+   for(i=nrl; i<= nrh; i++)
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+     for(k=ncolol; k<=ncoloh; k++){
-   double age, agelim, hf;
+       out[i][k]=0.;
-   double ***p3matp, ***p3matm, ***varhe;
+       for(j=ncl; j<=nch; j++)
-   double **dnewm,**doldm;
+         out[i][k] +=in[i][j]*b[j][k];
-   double *xp, *xm;
+     }
-   double **gp, **gm;
+   return out;
-   double ***gradg, ***trgradg;
+ }
-   int theta;
-   double eip, vip;
+ /************* Higher Matrix Product ***************/
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
-   xp=vector(1,npar);
+ {
-   xm=vector(1,npar);
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+      'nhstepm*hstepm*stepm' months (i.e. until
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
-   pstamp(ficresstdeij);
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+      (typically every 2 years instead of every month which is too big
-   fprintf(ficresstdeij,"# Age");
+      for the memory).
-   for(i=1; i<=nlstate;i++){
+      Model is determined by parameters x and covariates have to be
-     for(j=1; j<=nlstate;j++)
+      included manually here.
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-     fprintf(ficresstdeij," e%1d. ",i);
+      */
-   }
-   fprintf(ficresstdeij,"\n");
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
-   pstamp(ficrescveij);
+   double **newm;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   double agexact;
-   fprintf(ficrescveij,"# Age");
+   double agebegin, ageend;
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++){
+   /* Hstepm could be zero and should return the unit matrix */
-       cptj= (j-1)*nlstate+i;
+   for (i=1;i<=nlstate+ndeath;i++)
-       for(i2=1; i2<=nlstate;i2++)
+     for (j=1;j<=nlstate+ndeath;j++){
-         for(j2=1; j2<=nlstate;j2++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-           cptj2= (j2-1)*nlstate+i2;
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-           if(cptj2 <= cptj)
+     }
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         }
+   for(h=1; h <=nhstepm; h++){
-     }
+     for(d=1; d <=hstepm; d++){
-   fprintf(ficrescveij,"\n");
+       newm=savm;
+       /* Covariates have to be included here again */
-   if(estepm < stepm){
+       cov[1]=1.;
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-   }
+       cov[2]=agexact;
-   else  hstepm=estepm;
+       if(nagesqr==1)
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+         cov[3]= agexact*agexact;
-    * This is mainly to measure the difference between two models: for example
+       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-    * progression in between and thus overestimating or underestimating according
+         /* printf("hpxij 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)); */
-    * to the curvature of the survival function. If, for the same date, we
+       }
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-    * to compare the new estimate of Life expectancy with the same linear
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-    * hypothesis. A more precise result, taking into account a more precise
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-    * curvature will be obtained if estepm is as small as stepm. */
+         /* 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 example we decided to compute the life expectancy with the smallest unit */
+       for (k=1; k<=cptcovage;k++){
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+         if(Dummy[Tvar[Tage[k]]]){
-      nhstepm is the number of hstepm from age to agelim
+           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-      nstepm is the number of stepm from age to agelin.
+         } else{
-      Look at hpijx to understand the reason of that which relies in memory size
+           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
-      and note for a fixed period like estepm months */
+         }
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+         /* 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]); */
-      survival function given by stepm (the optimization length). Unfortunately it
+       }
-      means that if the survival funtion is printed only each two years of age and if
+       for (k=1; k<=cptcovprod;k++){ /*  */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+         /* printf("hPxij 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]); */
-      results. So we changed our mind and took the option of the best precision.
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-   */
+       }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       /* for (k=1; k<=cptcovn;k++)  */
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-   /* If stepm=6 months */
+       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
-   /* nhstepm age range expressed in number of stepm */
+       /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
-   agelim=AGESUP;
+       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                         /* right multiplication of oldm by the current matrix */
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+       /* if((int)age == 70){ */
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
-   for (age=bage; age<=fage; age ++){
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       /*          } */
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
-     /* Computing  Variances of health expectancies */
+       /*          printf("\n"); */
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+       /*        } */
-        decrease memory allocation */
+       /* } */
-     for(theta=1; theta <=npar; theta++){
+       savm=oldm;
-       for(i=1; i<=npar; i++){
+       oldm=newm;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     }
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+     for(i=1; i<=nlstate+ndeath; i++)
-       }
+       for(j=1;j<=nlstate+ndeath;j++) {
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+         po[i][j][h]=newm[i][j];
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
-       for(j=1; j<= nlstate; j++){
+     /*printf("h=%d ",h);*/
-         for(i=1; i<=nlstate; i++){
+   } /* end h */
-           for(h=0; h<=nhstepm-1; h++){
+   /*     printf("\n H=%d \n",h); */
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+   return po;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+ }
-           }
-         }
+ /************* 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(ij=1; ij<= nlstate*nlstate; ij++)
+ {
-         for(h=0; h<=nhstepm-1; h++){
+   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+      'nhstepm*hstepm*stepm' months (i.e. until
-         }
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-     }/* End theta */
+      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(h=0; h<=nhstepm-1; h++)
+      for the memory).
-       for(j=1; j<=nlstate*nlstate;j++)
+      Model is determined by parameters x and covariates have to be
-         for(theta=1; theta <=npar; theta++)
+      included manually here. Then we use a call to bmij(x and cov)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
+   */
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   int i, j, d, h, k;
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+   double **out, cov[NCOVMAX+1], **bmij();
-         varhe[ij][ji][(int)age] =0.;
+   double **newm, ***newmm;
+   double agexact;
-      printf("%d|",(int)age);fflush(stdout);
+   double agebegin, ageend;
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   double **oldm, **savm;
-      for(h=0;h<=nhstepm-1;h++){
-       for(k=0;k<=nhstepm-1;k++){
+   newmm=po; /* To be saved */
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+   oldm=oldms;savm=savms; /* Global pointers */
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+   /* Hstepm could be zero and should return the unit matrix */
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+   for (i=1;i<=nlstate+ndeath;i++)
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+     for (j=1;j<=nlstate+ndeath;j++){
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+       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 */
-     /* Computing expectancies */
+   for(h=1; h <=nhstepm; h++){
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     for(d=1; d <=hstepm; d++){
-     for(i=1; i<=nlstate;i++)
+       newm=savm;
-       for(j=1; j<=nlstate;j++)
+       /* Covariates have to be included here again */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+       cov[1]=1.;
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+       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 *\/ */
-           /* 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]);*/
+       cov[2]=agexact;
+       if(nagesqr==1)
-         }
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++){
-     fprintf(ficresstdeij,"%3.0f",age );
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-     for(i=1; i<=nlstate;i++){
+       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
-       eip=0.;
+         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-       vip=0.;
+         /* 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(j=1; j<=nlstate;j++){
+       }
-         eip += eij[i][j][(int)age];
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+         /* 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]); */
        }
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
-     }
+         if(Dummy[Tvar[Tage[k]]]){
-     fprintf(ficresstdeij,"\n");
+           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         } else{
-     fprintf(ficrescveij,"%3.0f",age );
+           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
-     for(i=1; i<=nlstate;i++)
+         }
-       for(j=1; j<=nlstate;j++){
+         /* 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]); */
-         cptj= (j-1)*nlstate+i;
+       }
-         for(i2=1; i2<=nlstate;i2++)
+       for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
-           for(j2=1; j2<=nlstate;j2++){
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-             cptj2= (j2-1)*nlstate+i2;
+       }
-             if(cptj2 <= cptj)
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-           }
-       }
+       /* Careful transposed matrix */
-     fprintf(ficrescveij,"\n");
+       /* 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); */
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+       /* if((int)age == 70){ */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /*          printf("%d pmmij ",i); */
-   printf("\n");
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-   fprintf(ficlog,"\n");
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
-   free_vector(xm,1,npar);
+       /*          printf(" oldm "); */
-   free_vector(xp,1,npar);
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+       /*            printf("%f ",oldm[i][j]); */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+       /*          } */
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+       /*          printf("\n"); */
- }
+       /*        } */
+       /* } */
- /************ Variance ******************/
+       savm=oldm;
- 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[])
+       oldm=newm;
- {
+     }
-   /* Variance of health expectancies */
+     for(i=1; i<=nlstate+ndeath; i++)
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+       for(j=1;j<=nlstate+ndeath;j++) {
-   /* double **newm;*/
+         po[i][j][h]=newm[i][j];
-   double **dnewm,**doldm;
+         /* if(h==nhstepm) */
-   double **dnewmp,**doldmp;
+         /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
-   int i, j, nhstepm, hstepm, h, nstepm ;
+       }
-   int k, cptcode;
+     /* printf("h=%d %.1f ",h, agexact); */
-   double *xp;
+   } /* end h */
-   double **gp, **gm;  /* for var eij */
+   /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
-   double ***gradg, ***trgradg; /*for var eij */
+   return po;
-   double **gradgp, **trgradgp; /* for var p point j */
+ }
-   double *gpp, *gmp; /* for var p point j */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   double ***p3mat;
+ #ifdef NLOPT
-   double age,agelim, hf;
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-   double ***mobaverage;
+   double fret;
-   int theta;
+   double *xt;
-   char digit[4];
+   int j;
-   char digitp[25];
+   myfunc_data *d2 = (myfunc_data *) pd;
+ /* xt = (p1-1); */
-   char fileresprobmorprev[FILENAMELENGTH];
+   xt=vector(1,n);
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   if(popbased==1){
-     if(mobilav!=0)
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-       strcpy(digitp,"-populbased-mobilav-");
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-     else strcpy(digitp,"-populbased-nomobil-");
+   printf("Function = %.12lf ",fret);
-   }
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   else
+   printf("\n");
-     strcpy(digitp,"-stablbased-");
+  free_vector(xt,1,n);
+   return fret;
-   if (mobilav!=0) {
+ }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ #endif
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /*************** log-likelihood *************/
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ double func( double *x)
-     }
+ {
-   }
+   int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
-   strcpy(fileresprobmorprev,"prmorprev");
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   sprintf(digit,"%-d",ij);
+   double **out;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   double lli; /* Individual log likelihood */
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   int s1, s2;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
-   strcat(fileresprobmorprev,fileres);
+   double bbh, survp;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   long ipmx;
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   double agexact;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   /*extern weight */
-   }
+   /* We are differentiating ll according to initial status */
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     printf(" %d\n",s[4][i]);
-   pstamp(ficresprobmorprev);
+   */
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   ++countcallfunc;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   cov[1]=1.;
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   }
+   ioffset=0;
-   fprintf(ficresprobmorprev,"\n");
+   if(mle==1){
-   fprintf(ficgp,"\n# Routine varevsij");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+       /* Computes the values of the ncovmodel covariates of the model
-   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");
+          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+          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.
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       */
-   pstamp(ficresvij);
+       ioffset=2+nagesqr ;
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+    /* Fixed */
-   if(popbased==1)
+       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
-   else
+       }
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   fprintf(ficresvij,"# Age");
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-   for(i=1; i<=nlstate;i++)
+          has been calculated etc */
-     for(j=1; j<=nlstate;j++)
+       /* For an individual i, wav[i] gives the number of effective waves */
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+       /* We compute the contribution to Likelihood of each effective transition
-   fprintf(ficresvij,"\n");
+          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];
-   xp=vector(1,npar);
+          s2=s[mw[mi+1][i]][i];
-   dnewm=matrix(1,nlstate,1,npar);
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
-   doldm=matrix(1,nlstate,1,nlstate);
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-   gpp=vector(nlstate+1,nlstate+ndeath);
+           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
-   gmp=vector(nlstate+1,nlstate+ndeath);
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+         }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   if(estepm < stepm){
+           for (j=1;j<=nlstate+ndeath;j++){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   else  hstepm=estepm;
+           }
-   /* For example we decided to compute the life expectancy with the smallest unit */
+         for(d=0; d<dh[mi][i]; d++){
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+           newm=savm;
-      nhstepm is the number of hstepm from age to agelim
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-      nstepm is the number of stepm from age to agelin.
+           cov[2]=agexact;
-      Look at hpijx to understand the reason of that which relies in memory size
+           if(nagesqr==1)
-      and note for a fixed period like k years */
+             cov[3]= agexact*agexact;  /* Should be changed here */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+           for (kk=1; kk<=cptcovage;kk++) {
-      survival function given by stepm (the optimization length). Unfortunately it
+           if(!FixedV[Tvar[Tage[kk]]])
-      means that if the survival funtion is printed every two years of age and if
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+           else
-      results. So we changed our mind and took the option of the best precision.
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
-   */
+           }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   agelim = AGESUP;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+           savm=oldm;
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           oldm=newm;
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         } /* end mult */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-     gp=matrix(0,nhstepm,1,nlstate);
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-     gm=matrix(0,nhstepm,1,nlstate);
+          * 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
-     for(theta=1; theta <=npar; theta++){
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+          * 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
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+                                  * -stepm/2 to stepm/2 .
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+                                  * 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.
-       if (popbased==1) {
+                                  */
-         if(mobilav ==0){
+         s1=s[mw[mi][i]][i];
-           for(i=1; i<=nlstate;i++)
+         s2=s[mw[mi+1][i]][i];
-             prlim[i][i]=probs[(int)age][i][ij];
+         bbh=(double)bh[mi][i]/(double)stepm;
-         }else{ /* mobilav */
+         /* bias bh is positive if real duration
-           for(i=1; i<=nlstate;i++)
+          * is higher than the multiple of stepm and negative otherwise.
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+          */
-         }
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-       }
+         if( s2 > nlstate){
+           /* i.e. if s2 is a death state and if the date of death is known
-       for(j=1; j<= nlstate; j++){
+              then the contribution to the likelihood is the probability to
-         for(h=0; h<=nhstepm; h++){
+              die between last step unit time and current  step unit time,
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+              which is also equal to probability to die before dh
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+              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
-       /* This for computing probability of death (h=1 means
+              health state: the date of the interview describes the actual state
-          computed over hstepm matrices product = hstepm*stepm months)
+              and not the date of a change in health state. The former idea was
-          as a weighted average of prlim.
+              to consider that at each interview the state was recorded
-       */
+              (healthy, disable or death) and IMaCh was corrected; but when we
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+              introduced the exact date of death then we should have modified
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+              the contribution of an exact death to the likelihood. This new
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+              contribution is smaller and very dependent of the step unit
-       }
+              stepm. It is no more the probability to die between last interview
-       /* end probability of death */
+              and month of death but the probability to survive from last
+              interview up to one month before death multiplied by the
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+              probability to die within a month. Thanks to Chris
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+              Jackson for correcting this bug.  Former versions increased
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+              mortality artificially. The bad side is that we add another loop
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+              which slows down the processing. The difference can be up to 10%
+              lower mortality.
-       if (popbased==1) {
+           */
-         if(mobilav ==0){
+           /* If, at the beginning of the maximization mostly, the
-           for(i=1; i<=nlstate;i++)
+              cumulative probability or probability to be dead is
-             prlim[i][i]=probs[(int)age][i][ij];
+              constant (ie = 1) over time d, the difference is equal to
-         }else{ /* mobilav */
+.  out[s1][3] = savm[s1][3]: probability, being at state
-           for(i=1; i<=nlstate;i++)
+              s1 at precedent wave, to be dead a month before current
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+              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,
-       for(j=1; j<= nlstate; j++){
+              it should be very low but not zero otherwise the log go to
-         for(h=0; h<=nhstepm; h++){
+              infinity.
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+           */
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+ /* #ifdef INFINITYORIGINAL */
-         }
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-       }
+ /* #else */
-       /* This for computing probability of death (h=1 means
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-          computed over hstepm matrices product = hstepm*stepm months)
+ /*          lli=log(mytinydouble); */
-          as a weighted average of prlim.
+ /*        else */
-       */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+ /* #endif */
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+           lli=log(out[s1][s2] - savm[s1][s2]);
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+         } else if  ( s2==-1 ) { /* alive */
-       /* end probability of death */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       for(j=1; j<= nlstate; j++) /* vareij */
+           /*survp += out[s1][j]; */
-         for(h=0; h<=nhstepm; h++){
+           lli= log(survp);
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
-         }
+         else if  (s2==-4) {
+           for (j=3,survp=0. ; j<=nlstate; j++)
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+           lli= log(survp);
-       }
+         }
+         else if  (s2==-5) {
-     } /* End theta */
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+           lli= log(survp);
+         }
-     for(h=0; h<=nhstepm; h++) /* veij */
+         else{
-       for(j=1; j<=nlstate;j++)
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-         for(theta=1; theta <=npar; theta++)
+           /*  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 */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+         }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+         /*if(lli ==000.0)*/
-       for(theta=1; theta <=npar; theta++)
+         /*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); */
-         trgradgp[j][theta]=gradgp[theta][j];
+         ipmx +=1;
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+         /* if (lli < log(mytinydouble)){ */
-     for(i=1;i<=nlstate;i++)
+         /*   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); */
-       for(j=1;j<=nlstate;j++)
+         /*   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]); */
-         vareij[i][j][(int)age] =0.;
+         /* } */
+       } /* end of wave */
-     for(h=0;h<=nhstepm;h++){
+     } /* end of individual */
-       for(k=0;k<=nhstepm;k++){
+   }  else if(mle==2){
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         for(i=1;i<=nlstate;i++)
+       for(mi=1; mi<= wav[i]-1; mi++){
-           for(j=1;j<=nlstate;j++)
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+           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);
+           }
-     /* pptj */
+         for(d=0; d<=dh[mi][i]; d++){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+           newm=savm;
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+           cov[2]=agexact;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+           if(nagesqr==1)
-         varppt[j][i]=doldmp[j][i];
+             cov[3]= agexact*agexact;
-     /* end ppptj */
+           for (kk=1; kk<=cptcovage;kk++) {
-     /*  x centered again */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+           }
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     if (popbased==1) {
+           savm=oldm;
-       if(mobilav ==0){
+           oldm=newm;
-         for(i=1; i<=nlstate;i++)
+         } /* end mult */
-           prlim[i][i]=probs[(int)age][i][ij];
-       }else{ /* mobilav */
+         s1=s[mw[mi][i]][i];
-         for(i=1; i<=nlstate;i++)
+         s2=s[mw[mi+1][i]][i];
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+         bbh=(double)bh[mi][i]/(double)stepm;
-       }
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-     }
+         ipmx +=1;
+         sw += weight[i];
-     /* This for computing probability of death (h=1 means
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+       } /* end of wave */
-        as a weighted average of prlim.
+     } /* end of individual */
-     */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       for(mi=1; mi<= wav[i]-1; mi++){
-     }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     /* end probability of death */
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+           }
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+         for(d=0; d<dh[mi][i]; d++){
-       for(i=1; i<=nlstate;i++){
+           newm=savm;
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       }
+           cov[2]=agexact;
-     }
+           if(nagesqr==1)
-     fprintf(ficresprobmorprev,"\n");
+             cov[3]= agexact*agexact;
+           for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(ficresvij,"%.0f ",age );
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-     for(i=1; i<=nlstate;i++)
+           }
-       for(j=1; j<=nlstate;j++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       }
+           savm=oldm;
-     fprintf(ficresvij,"\n");
+           oldm=newm;
-     free_matrix(gp,0,nhstepm,1,nlstate);
+         } /* end mult */
-     free_matrix(gm,0,nhstepm,1,nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+         s1=s[mw[mi][i]][i];
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+         s2=s[mw[mi+1][i]][i];
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         bbh=(double)bh[mi][i]/(double)stepm;
-   } /* End age */
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+         ipmx +=1;
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+         sw += weight[i];
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+       } /* end of wave */
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     } /* end of individual */
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       for(mi=1; mi<= wav[i]-1; mi++){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+           for (j=1;j<=nlstate+ndeath;j++){
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   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);
+         for(d=0; d<dh[mi][i]; d++){
-   /*  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);
+           newm=savm;
- */
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+           cov[2]=agexact;
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-   free_vector(xp,1,npar);
+           for (kk=1; kk<=cptcovage;kk++) {
-   free_matrix(doldm,1,nlstate,1,nlstate);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   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);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           savm=oldm;
-   fclose(ficresprobmorprev);
+           oldm=newm;
-   fflush(ficgp);
+         } /* end mult */
-   fflush(fichtm);
- }  /* end varevsij */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
- /************ Variance of prevlim ******************/
+         if( s2 > nlstate){
- 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[])
+           lli=log(out[s1][s2] - savm[s1][s2]);
- {
+         } else if  ( s2==-1 ) { /* alive */
-   /* Variance of prevalence limit */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+             survp += out[s1][j];
-   double **newm;
+           lli= log(survp);
-   double **dnewm,**doldm;
+         }else{
-   int i, j, nhstepm, hstepm;
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   int k, cptcode;
+         }
-   double *xp;
+         ipmx +=1;
-   double *gp, *gm;
+         sw += weight[i];
-   double **gradg, **trgradg;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double age,agelim;
+ /*      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]); */
-   int theta;
+       } /* end of wave */
+     } /* end of individual */
-   pstamp(ficresvpl);
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficresvpl,"# Age");
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   for(i=1; i<=nlstate;i++)
+       for(mi=1; mi<= wav[i]-1; mi++){
-       fprintf(ficresvpl," %1d-%1d",i,i);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   fprintf(ficresvpl,"\n");
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   xp=vector(1,npar);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   dnewm=matrix(1,nlstate,1,npar);
+           }
-   doldm=matrix(1,nlstate,1,nlstate);
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   hstepm=1*YEARM; /* Every year of age */
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+           cov[2]=agexact;
-   agelim = AGESUP;
+           if(nagesqr==1)
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+             cov[3]= agexact*agexact;
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           for (kk=1; kk<=cptcovage;kk++) {
-     if (stepm >= YEARM) hstepm=1;
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           }
-     gradg=matrix(1,npar,1,nlstate);
-     gp=vector(1,nlstate);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     gm=vector(1,nlstate);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-     for(theta=1; theta <=npar; theta++){
+           oldm=newm;
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+         } /* end mult */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       }
+         s1=s[mw[mi][i]][i];
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+         s2=s[mw[mi+1][i]][i];
-       for(i=1;i<=nlstate;i++)
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         gp[i] = prlim[i][i];
+         ipmx +=1;
+         sw += weight[i];
-       for(i=1; i<=npar; i++) /* Computes gradient */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         /*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]);*/
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       } /* end of wave */
-       for(i=1;i<=nlstate;i++)
+     } /* end of individual */
-         gm[i] = prlim[i][i];
+   } /* End of if */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-       for(i=1;i<=nlstate;i++)
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     } /* End theta */
+   return -l;
+ }
-     trgradg =matrix(1,nlstate,1,npar);
+ /*************** log-likelihood *************/
-     for(j=1; j<=nlstate;j++)
+ double funcone( double *x)
-       for(theta=1; theta <=npar; theta++)
+ {
-         trgradg[j][theta]=gradg[theta][j];
+   /* Same as func but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
-     for(i=1;i<=nlstate;i++)
+   int ioffset=0;
-       varpl[i][(int)age] =0.;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   double **out;
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   double lli; /* Individual log likelihood */
-     for(i=1;i<=nlstate;i++)
+   double llt;
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   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 */
-     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+   double bbh, survp;
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   double agexact;
-     fprintf(ficresvpl,"\n");
+   double agebegin, ageend;
-     free_vector(gp,1,nlstate);
+   /*extern weight */
-     free_vector(gm,1,nlstate);
+   /* We are differentiating ll according to initial status */
-     free_matrix(gradg,1,npar,1,nlstate);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-     free_matrix(trgradg,1,nlstate,1,npar);
+   /*for(i=1;i<imx;i++)
-   } /* End age */
+     printf(" %d\n",s[4][i]);
+   */
-   free_vector(xp,1,npar);
+   cov[1]=1.;
-   free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
- }
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /* ioffset=2+nagesqr+cptcovage; */
- /************ Variance of one-step probabilities  ******************/
+     ioffset=2+nagesqr;
- 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[])
+     /* Fixed */
- {
+     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
-   int i, j=0,  i1, k1, l1, t, tj;
+     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
-   int k2, l2, j1,  z1;
+     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
-   int k=0,l, cptcode;
+       cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
-   int first=1, first1;
+ /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+ /*    cov[2+6]=covar[Tvar[6]][i];  */
-   double **dnewm,**doldm;
+ /*    cov[2+6]=covar[2][i]; V2  */
-   double *xp;
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
-   double *gp, *gm;
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
-   double **gradg, **trgradg;
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
-   double **mu;
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
-   double age,agelim, cov[NCOVMAX];
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+ /*    cov[2+9]=covar[1][i]; V1  */
-   int theta;
+     }
-   char fileresprob[FILENAMELENGTH];
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
-   char fileresprobcov[FILENAMELENGTH];
+     /*   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?)*\/ */
-   char fileresprobcor[FILENAMELENGTH];
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
-   double ***varpij;
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
+     /* } */
-   strcpy(fileresprob,"prob");
-   strcat(fileresprob,fileres);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
-     printf("Problem with resultfile: %s\n", fileresprob);
+     /* Wave varying (but not age varying) */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+       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]; */
-   strcpy(fileresprobcov,"probcov");
+         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
-   strcat(fileresprobcov,fileres);
+       }
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
-   }
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
-   strcpy(fileresprobcor,"probcor");
+       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
-   strcat(fileresprobcor,fileres);
+       /* 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]); */
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+       /*        /\* 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]; */
-   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);
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+         for (j=1;j<=nlstate+ndeath;j++){
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+         }
-   pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
-   fprintf(ficresprob,"# Age");
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
-   pstamp(ficresprobcov);
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
-   fprintf(ficresprobcov,"# Age");
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   pstamp(ficresprobcor);
+           and mw[mi+1][i]. dh depends on stepm.*/
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+         newm=savm;
-   fprintf(ficresprobcor,"# Age");
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
+         cov[2]=agexact;
+         if(nagesqr==1)
-   for(i=1; i<=nlstate;i++)
+           cov[3]= agexact*agexact;
-     for(j=1; j<=(nlstate+ndeath);j++){
+         for (kk=1; kk<=cptcovage;kk++) {
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+           if(!FixedV[Tvar[Tage[kk]]])
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+           else
-     }
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
-  /* fprintf(ficresprob,"\n");
+         }
-   fprintf(ficresprobcov,"\n");
+         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
-   fprintf(ficresprobcor,"\n");
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-  */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-  xp=vector(1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+         savm=oldm;
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+         oldm=newm;
-   first=1;
+       } /* end mult */
-   fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+       s1=s[mw[mi][i]][i];
-   fprintf(fichtm,"\n");
+       s2=s[mw[mi+1][i]][i];
+       /* if(s2==-1){ */
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+       /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+       /*        /\* exit(1); *\/ */
-   file %s<br>\n",optionfilehtmcov);
+       /* } */
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+       bbh=(double)bh[mi][i]/(double)stepm;
- and drawn. It helps understanding how is the covariance between two incidences.\
+       /* bias is positive if real duration
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+        * is higher than the multiple of stepm and negative otherwise.
-   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 \
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+         lli=log(out[s1][s2] - savm[s1][s2]);
- standard deviations wide on each axis. <br>\
+       } else if  ( s2==-1 ) { /* alive */
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+         for (j=1,survp=0. ; j<=nlstate; j++)
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+         lli= log(survp);
+       }else if (mle==1){
-   cov[1]=1;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   tj=cptcoveff;
+       } else if(mle==2){
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+         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 */
-   j1=0;
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   for(t=1; t<=tj;t++){
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-     for(i1=1; i1<=ncodemax[t];i1++){
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-       j1++;
+         lli=log(out[s1][s2]); /* Original formula */
-       if  (cptcovn>0) {
+       } else{  /* mle=0 back to 1 */
-         fprintf(ficresprob, "\n#********** Variable ");
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-         fprintf(ficresprob, "**********\n#\n");
+       } /* End of if */
-         fprintf(ficresprobcov, "\n#********** Variable ");
+       ipmx +=1;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       sw += weight[i];
-         fprintf(ficresprobcov, "**********\n#\n");
+       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]); */
-         fprintf(ficgp, "\n#********** Variable ");
+       if(globpr){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
-         fprintf(ficgp, "**********\n#\n");
+  %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,
+*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+           llt +=ll[k]*gipmx/gsw;
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
-         fprintf(ficresprobcor, "\n#********** Variable ");
+         fprintf(ficresilk," %10.6f\n", -llt);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       }
-         fprintf(ficresprobcor, "**********\n#");
+         } /* end of wave */
-       }
+ } /* end of individual */
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-       for (age=bage; age<=fage; age ++){
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-         cov[2]=age;
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-         for (k=1; k<=cptcovn;k++) {
+ if(globpr==0){ /* First time we count the contributions and weights */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         gipmx=ipmx;
-         }
+         gsw=sw;
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ }
-         for (k=1; k<=cptcovprod;k++)
+ return -l;
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ }
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ /*************** function likelione ***********/
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+ {
+   /* This routine should help understanding what is done with
-         for(theta=1; theta <=npar; theta++){
+      the selection of individuals/waves and
-           for(i=1; i<=npar; i++)
+      to check the exact contribution to the likelihood.
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+      Plotting could be done.
+    */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   int k;
-           k=0;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-           for(i=1; i<= (nlstate); i++){
+     strcpy(fileresilk,"ILK_");
-             for(j=1; j<=(nlstate+ndeath);j++){
+     strcat(fileresilk,fileresu);
-               k=k+1;
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-               gp[k]=pmmij[i][j];
+       printf("Problem with resultfile: %s\n", fileresilk);
-             }
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-           }
+     }
+     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");
-           for(i=1; i<=npar; i++)
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+     /*  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++)
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-           k=0;
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-           for(i=1; i<=(nlstate); i++){
+   }
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+   *fretone=(*func)(p);
-               gm[k]=pmmij[i][j];
+   if(*globpri !=0){
-             }
+     fclose(ficresilk);
-           }
+     if (mle ==0)
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+     else if(mle >=1)
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+       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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-           for(theta=1; theta <=npar; theta++)
+     for (k=1; k<= nlstate ; k++) {
-             trgradg[j][theta]=gradg[theta][j];
+       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);
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+     }
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+     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> \
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     fflush(fichtm);
+   }
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+   return;
+ }
-         k=0;
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
+ /*********** Maximum Likelihood Estimation ***************/
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-           }
+ {
-         }
+   int i,j, iter=0;
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   double **xi;
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   double fret;
-             varpij[i][j][(int)age] = doldm[i][j];
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ #ifdef NLOPT
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   int creturn;
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   nlopt_opt opt;
-           }*/
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
+   double *lb;
-         fprintf(ficresprob,"\n%d ",(int)age);
+   double minf; /* the minimum objective value, upon return */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+   myfunc_data dinst, *d = &dinst;
+ #endif
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+   xi=matrix(1,npar,1,npar);
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+   for (i=1;i<=npar;i++)
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+     for (j=1;j<=npar;j++)
-         }
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-         i=0;
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-         for (k=1; k<=(nlstate);k++){
+   strcpy(filerespow,"POW_");
-           for (l=1; l<=(nlstate+ndeath);l++){
+   strcat(filerespow,fileres);
-             i=i++;
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+     printf("Problem with resultfile: %s\n", filerespow);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-             for (j=1; j<=i;j++){
+   }
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+   for (i=1;i<=nlstate;i++)
-             }
+     for(j=1;j<=nlstate+ndeath;j++)
-           }
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-         }/* end of loop for state */
+   fprintf(ficrespow,"\n");
-       } /* end of loop for age */
+ #ifdef POWELL
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-       /* Confidence intervalle of pij  */
+ #endif
-       /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+ #ifdef NLOPT
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+ #ifdef NEWUOA
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-         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);
+ #else
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+ #endif
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+   lb=vector(0,npar-1);
-       */
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+   nlopt_set_initial_step1(opt, 0.1);
-       first1=1;
-       for (k2=1; k2<=(nlstate);k2++){
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+   d->function = func;
-           if(l2==k2) continue;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-           j=(k2-1)*(nlstate+ndeath)+l2;
+   nlopt_set_min_objective(opt, myfunc, d);
-           for (k1=1; k1<=(nlstate);k1++){
+   nlopt_set_xtol_rel(opt, ftol);
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-               if(l1==k1) continue;
+     printf("nlopt failed! %d\n",creturn);
-               i=(k1-1)*(nlstate+ndeath)+l1;
+   }
-               if(i<=j) continue;
+   else {
-               for (age=bage; age<=fage; age ++){
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-                 if ((int)age %5==0){
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+     iter=1; /* not equal */
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   }
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   nlopt_destroy(opt);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+ #endif
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+   free_matrix(xi,1,npar,1,npar);
-                   c12=cv12/sqrt(v1*v2);
+   fclose(ficrespow);
-                   /* Computing eigen value of matrix of covariance */
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-                   /* Eigen vectors */
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+ }
-                   /*v21=sqrt(1.-v11*v11); *//* error */
-                   v21=(lc1-v1)/cv12*v11;
+ /**** Computes Hessian and covariance matrix ***/
-                   v12=-v21;
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-                   v22=v11;
+ {
-                   tnalp=v21/v11;
+   double  **a,**y,*x,pd;
-                   if(first1==1){
+   /* double **hess; */
-                     first1=0;
+   int i, j;
-                     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);
+   int *indx;
-                   }
-                   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);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-                   /*printf(fignu*/
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-                   if(first==1){
+   double gompertz(double p[]);
-                     first=0;
+   /* hess=matrix(1,npar,1,npar); */
-                     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);
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+   for (i=1;i<=npar;i++){
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+     printf("%d-",i);fflush(stdout);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-                     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);
+     /*  printf(" %f ",p[i]);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-                     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",\
+   for (i=1;i<=npar;i++) {
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+     for (j=1;j<=npar;j++)  {
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+       if (j>i) {
-                   }else{
+         printf(".%d-%d",i,j);fflush(stdout);
-                     first=0;
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
-                     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);
+         hess[j][i]=hess[i][j];
-                     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",\
+         /*printf(" %lf ",hess[i][j]);*/
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       }
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+     }
-                   }/* if first */
+   }
-                 } /* age mod 5 */
+   printf("\n");
-               } /* end loop age */
+   fprintf(ficlog,"\n");
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-               first=1;
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-             } /*l12 */
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-           } /* k12 */
-         } /*l1 */
+   a=matrix(1,npar,1,npar);
-       }/* k1 */
+   y=matrix(1,npar,1,npar);
-     } /* loop covariates */
+   x=vector(1,npar);
-   }
+   indx=ivector(1,npar);
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   for (i=1;i<=npar;i++)
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   ludcmp(a,npar,indx,&pd);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_vector(xp,1,npar);
+   for (j=1;j<=npar;j++) {
-   fclose(ficresprob);
+     for (i=1;i<=npar;i++) x[i]=0;
-   fclose(ficresprobcov);
+     x[j]=1;
-   fclose(ficresprobcor);
+     lubksb(a,npar,indx,x);
-   fflush(ficgp);
+     for (i=1;i<=npar;i++){
-   fflush(fichtmcov);
+       matcov[i][j]=x[i];
- }
+     }
+   }
- /******************* Printing html file ***********/
+   printf("\n#Hessian matrix#\n");
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-                   int lastpass, int stepm, int weightopt, char model[],\
+   for (i=1;i<=npar;i++) {
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     for (j=1;j<=npar;j++) {
-                   int popforecast, int estepm ,\
+       printf("%.6e ",hess[i][j]);
-                   double jprev1, double mprev1,double anprev1, \
+       fprintf(ficlog,"%.6e ",hess[i][j]);
-                   double jprev2, double mprev2,double anprev2){
+     }
-   int jj1, k1, i1, cpt;
+     printf("\n");
+     fprintf(ficlog,"\n");
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   }
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
- </ul>");
+   /* printf("\n#Covariance matrix#\n"); */
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   /* fprintf(ficlog,"\n#Covariance matrix#\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 ",
+   /* for (i=1;i<=npar;i++) {  */
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   /*   for (j=1;j<=npar;j++) {  */
-    fprintf(fichtm,"\
+   /*     printf("%.6e ",matcov[i][j]); */
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   /*   } */
-    fprintf(fichtm,"\
+   /*   printf("\n"); */
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+   /*   fprintf(ficlog,"\n"); */
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   /* } */
-    fprintf(fichtm,"\
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+   /* Recompute Inverse */
-    <a href=\"%s\">%s</a> <br>\n",
+   /* for (i=1;i<=npar;i++) */
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-    fprintf(fichtm,"\
+   /* ludcmp(a,npar,indx,&pd); */
-  - Population projections by age and states: \
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
-  m=cptcoveff;
+   /*   x[j]=1; */
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   /*   lubksb(a,npar,indx,x); */
+   /*   for (i=1;i<=npar;i++){  */
-  jj1=0;
+   /*     y[i][j]=x[i]; */
-  for(k1=1; k1<=m;k1++){
+   /*     printf("%.3e ",y[i][j]); */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
-      jj1++;
+   /*   } */
-      if (cptcovn > 0) {
+   /*   printf("\n"); */
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   /*   fprintf(ficlog,"\n"); */
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   /* } */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   /* Verifying the inverse matrix */
-      }
+ #ifdef DEBUGHESS
-      /* Pij */
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
-      /* Quasi-incidences */
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+   for (j=1;j<=npar;j++) {
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+     for (i=1;i<=npar;i++){
-        /* Period (stable) prevalence in each health state */
+       printf("%.2f ",y[i][j]);
-        for(cpt=1; cpt<nlstate;cpt++){
+       fprintf(ficlog,"%.2f ",y[i][j]);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+     }
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+     printf("\n");
-        }
+     fprintf(ficlog,"\n");
-      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 : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+ #endif
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-      }
+   free_matrix(a,1,npar,1,npar);
-    } /* end i1 */
+   free_matrix(y,1,npar,1,npar);
-  }/* End k1 */
+   free_vector(x,1,npar);
-  fprintf(fichtm,"</ul>");
+   free_ivector(indx,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
-  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);
+ /*************** hessian matrix ****************/
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
-  fprintf(fichtm,"\
+   int i;
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   int l=1, lmax=20;
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   double k1,k2, res, fx;
+   double p2[MAXPARM+1]; /* identical to x */
-  fprintf(fichtm,"\
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   int k=0,kmax=10;
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   double l1;
-  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): \
+   fx=func(x);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-  fprintf(fichtm,"\
+     l1=pow(10,l);
-  - (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): \
+     delts=delt;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+     for(k=1 ; k <kmax; k=k+1){
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+       delt = delta*(l1*k);
-  fprintf(fichtm,"\
+       p2[theta]=x[theta] +delt;
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+       p2[theta]=x[theta]-delt;
-  fprintf(fichtm,"\
+       k2=func(p2)-fx;
-  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
-  fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+ #ifdef DEBUGHESSII
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+       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);
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+ #endif
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
- /*      <br>",fileres,fileres,fileres,fileres); */
+         k=kmax;
- /*  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); */
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-  fflush(fichtm);
+         k=kmax; l=lmax*10;
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+       }
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-  m=cptcoveff;
+         delts=delt;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       }
+     } /* End loop k */
-  jj1=0;
+   }
-  for(k1=1; k1<=m;k1++){
+   delti[theta]=delts;
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   return res;
-      jj1++;
-      if (cptcovn > 0) {
+ }
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+ {
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   int i;
-      }
+   int l=1, lmax=20;
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   double k1,k2,k3,k4,res,fx;
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   double p2[MAXPARM+1];
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   int k, kmax=1;
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   double v1, v2, cv12, lc1, lc2;
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   int firstime=0;
- health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+   fx=func(x);
-    } /* end i1 */
+   for (k=1; k<=kmax; k=k+10) {
-  }/* End k1 */
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-  fprintf(fichtm,"</ul>");
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-  fflush(fichtm);
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
- }
+     k1=func(p2)-fx;
- /******************* Gnuplot file **************/
+     p2[thetai]=x[thetai]+delti[thetai]*k;
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
+     k2=func(p2)-fx;
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-   int ng;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+     k3=func(p2)-fx;
- /*     printf("Problem with file %s",optionfilegnuplot); */
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+     p2[thetai]=x[thetai]-delti[thetai]*k;
- /*   } */
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
+     k4=func(p2)-fx;
-   /*#ifdef windows */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     if(k1*k2*k3*k4 <0.){
-     /*#endif */
+       firstime=1;
-   m=pow(2,cptcoveff);
+       kmax=kmax+10;
+     }
-   strcpy(dirfileres,optionfilefiname);
+     if(kmax >=10 || firstime ==1){
-   strcpy(optfileres,"vpl");
+       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);
-  /* 1eme*/
+       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);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+       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);
-    for (k1=1; k1<= m ; k1 ++) {
+       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);
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+     }
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+ #ifdef DEBUGHESSIJ
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+     v1=hess[thetai][thetai];
- set ylabel \"Probability\" \n\
+     v2=hess[thetaj][thetaj];
- set ter png small\n\
+     cv12=res;
- set size 0.65,0.65\n\
+     /* Computing eigen value of Hessian matrix */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+     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.;
-      for (i=1; i<= nlstate ; i ++) {
+     if ((lc2 <0) || (lc1 <0) ){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       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(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+       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);
-      for (i=1; i<= nlstate ; i ++) {
+     }
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ #endif
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   }
-      }
+   return res;
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ }
-      for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
-      }
+ /* { */
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+ /*   int i; */
-    }
+ /*   int l=1, lmax=20; */
-   }
+ /*   double k1,k2,k3,k4,res,fx; */
-   /*2 eme*/
+ /*   double p2[MAXPARM+1]; */
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
-   for (k1=1; k1<= m ; k1 ++) {
+ /*   int k=0,kmax=10; */
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+ /*   double l1; */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+ /*   fx=func(x); */
-     for (i=1; i<= nlstate+1 ; i ++) {
+ /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
-       k=2*i;
+ /*     l1=pow(10,l); */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+ /*     delts=delt; */
-       for (j=1; j<= nlstate+1 ; j ++) {
+ /*     for(k=1 ; k <kmax; k=k+1){ */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ /*       delt = delti*(l1*k); */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
-       }
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+ /*       k1=func(p2)-fx; */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ /*       k2=func(p2)-fx; */
-       }
-       fprintf(ficgp,"\" t\"\" w l 0,");
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-       for (j=1; j<= nlstate+1 ; j ++) {
+ /*       k3=func(p2)-fx; */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-       }
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+ /*       k4=func(p2)-fx; */
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+ /*       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); */
-   /*3eme*/
+ /* #endif */
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
-   for (k1=1; k1<= m ; k1 ++) {
+ /*      k=kmax; */
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+ /*       } */
-       /*       k=2+nlstate*(2*cpt-2); */
+ /*       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=2+(nlstate+1)*(cpt-1);
+ /*      k=kmax; l=lmax*10; */
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+ /*       } */
-       fprintf(ficgp,"set ter png small\n\
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
- set size 0.65,0.65\n\
+ /*      delts=delt; */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+ /*       } */
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ /*     } /\* End loop k *\/ */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ /*   } */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ /*   delti[theta]=delts; */
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ /*   return res;  */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ /* } */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       */
+ /************** Inverse of matrix **************/
-       for (i=1; i< nlstate ; i ++) {
+ void ludcmp(double **a, int n, int *indx, double *d)
-         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);*/
+   int i,imax,j,k;
+   double big,dum,sum,temp;
-       }
+   double *vv;
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-     }
+   vv=vector(1,n);
-   }
+   *d=1.0;
+   for (i=1;i<=n;i++) {
-   /* CV preval stable (period) */
+     big=0.0;
-   for (k1=1; k1<= m ; k1 ++) {
+     for (j=1;j<=n;j++)
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-       k=3;
+     if (big == 0.0){
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       printf(" Singular Hessian matrix at row %d:\n",i);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+       for (j=1;j<=n;j++) {
- set ter png small\nset size 0.65,0.65\n\
+         printf(" a[%d][%d]=%f,",i,j,a[i][j]);
- unset log y\n\
+         fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+       }
+       fflush(ficlog);
-       for (i=1; i< nlstate ; i ++)
+       fclose(ficlog);
-         fprintf(ficgp,"+$%d",k+i+1);
+       nrerror("Singular matrix in routine ludcmp");
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+     }
+     vv[i]=1.0/big;
-       l=3+(nlstate+ndeath)*cpt;
+   }
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+   for (j=1;j<=n;j++) {
-       for (i=1; i< nlstate ; i ++) {
+     for (i=1;i<j;i++) {
-         l=3+(nlstate+ndeath)*cpt;
+       sum=a[i][j];
-         fprintf(ficgp,"+$%d",l+i+1);
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-       }
+       a[i][j]=sum;
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+     }
-     }
+     big=0.0;
-   }
+     for (i=j;i<=n;i++) {
+       sum=a[i][j];
-   /* proba elementaires */
+       for (k=1;k<j;k++)
-   for(i=1,jk=1; i <=nlstate; i++){
+         sum -= a[i][k]*a[k][j];
-     for(k=1; k <=(nlstate+ndeath); k++){
+       a[i][j]=sum;
-       if (k != i) {
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-         for(j=1; j <=ncovmodel; j++){
+         big=dum;
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+         imax=i;
-           jk++;
+       }
-           fprintf(ficgp,"\n");
+     }
-         }
+     if (j != imax) {
-       }
+       for (k=1;k<=n;k++) {
-     }
+         dum=a[imax][k];
-    }
+         a[imax][k]=a[j][k];
+         a[j][k]=dum;
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+       }
-      for(jk=1; jk <=m; jk++) {
+       *d = -(*d);
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+       vv[imax]=vv[j];
-        if (ng==2)
+     }
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+     indx[j]=imax;
-        else
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+     if (j != n) {
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       dum=1.0/(a[j][j]);
-        i=1;
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-        for(k2=1; k2<=nlstate; k2++) {
+     }
-          k3=i;
+   }
-          for(k=1; k<=(nlstate+ndeath); k++) {
+   free_vector(vv,1,n);  /* Doesn't work */
-            if (k != k2){
+ ;
-              if(ng==2)
+ }
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-              else
+ void lubksb(double **a, int n, int *indx, double b[])
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+ {
-              ij=1;
+   int i,ii=0,ip,j;
-              for(j=3; j <=ncovmodel; j++) {
+   double sum;
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   for (i=1;i<=n;i++) {
-                  ij++;
+     ip=indx[i];
-                }
+     sum=b[ip];
-                else
+     b[ip]=b[i];
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     if (ii)
-              }
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-              fprintf(ficgp,")/(1");
+     else if (sum) ii=i;
+     b[i]=sum;
-              for(k1=1; k1 <=nlstate; k1++){
+   }
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+   for (i=n;i>=1;i--) {
-                ij=1;
+     sum=b[i];
-                for(j=3; j <=ncovmodel; j++){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     b[i]=sum/a[i][i];
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   }
-                    ij++;
+ }
-                  }
-                  else
+ void pstamp(FILE *fichier)
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+ {
-                }
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
-                fprintf(ficgp,")");
+ }
-              }
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-              i=i+ncovmodel;
+ /************ Frequencies ********************/
-            }
+ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
-          } /* end k */
+                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
-        } /* end k2 */
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-      } /* end jk */
+ {  /* Some frequencies as well as proposing some starting values */
-    } /* end ng */
-    fflush(ficgp);
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
- }  /* end gnuplot */
+   int iind=0, iage=0;
+   int mi; /* Effective wave */
+   int first;
- /*************** Moving average **************/
+   double ***freq; /* Frequencies */
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+   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 */
+   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);
-   int i, cpt, cptcod;
+   double *meanq, *stdq, *idq;
-   int modcovmax =1;
+   double **meanqt;
-   int mobilavrange, mob;
+   double *pp, **prop, *posprop, *pospropt;
-   double age;
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+   double agebegin, ageend;
-                            a covariate has 2 modalities */
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+   pp=vector(1,nlstate);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
-     if(mobilav==1) mobilavrange=5; /* default */
+   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
-     else mobilavrange=mobilav;
+   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
-     for (age=bage; age<=fage; age++)
+   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
-       for (i=1; i<=nlstate;i++)
+   stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+   idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+   meanqt=matrix(1,lastpass,1,nqtveff);
-     /* We keep the original values on the extreme ages bage, fage and for
+   strcpy(fileresp,"P_");
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+   strcat(fileresp,fileresu);
-        we use a 5 terms etc. until the borders are no more concerned.
+   /*strcat(fileresphtm,fileresu);*/
-     */
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-         for (i=1; i<=nlstate;i++){
+     exit(0);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+   }
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+     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));
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+     fflush(ficlog);
-           }
+     exit(70);
-         }
+   }
-       }/* end age */
+   else{
-     }/* end mob */
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-   }else return -1;
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
-   return 0;
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
- }/* End movingaverage */
+             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 and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
- /************** 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){
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
-   /* proj1, year, month, day of starting projection
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
-      agemin, agemax range of age
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-      anproj2 year of en of projection (same day and month as proj1).
+     fflush(ficlog);
-   */
+     exit(70);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+   } else{
-   int *popage;
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-   double agec; /* generic age */
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
-   double *popeffectif,*popcount;
+             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-   double ***p3mat;
+   }
-   double ***mobaverage;
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>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);
-   char fileresf[FILENAMELENGTH];
+   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
-   agelim=AGESUP;
+   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   j1=0;
-   strcpy(fileresf,"f");
-   strcat(fileresf,fileres);
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+   j=cptcoveff;  /* Only dummy covariates of the model */
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+      reference=low_education V1=0,V2=0
+      med_educ                V1=1 V2=0,
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+      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**cptcoveff
-   if (mobilav!=0) {
+   */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   dateintsum=0;
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   k2cpt=0;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   if(cptcoveff == 0 )
-     }
+     nl=1;  /* Constant and age model only */
-   }
+   else
+     nl=2;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=12) stepsize=1;
+   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
-   if(estepm < stepm){
+   /* Loop on nj=1 or 2 if dummy covariates j!=0
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    *   Loop on j1(1 to 2**cptcoveff) covariate combination
-   }
+    *     freq[s1][s2][iage] =0.
-   else  hstepm=estepm;
+    *     Loop on iind
+    *       ++freq[s1][s2][iage] weighted
-   hstepm=hstepm/stepm;
+    *     end iind
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+    *     if covariate and j!0
-                                fractional in yp1 */
+    *       headers Variable on one line
-   anprojmean=yp;
+    *     endif cov j!=0
-   yp2=modf((yp1*12),&yp);
+    *     header of frequency table by age
-   mprojmean=yp;
+    *     Loop on age
-   yp1=modf((yp2*30.5),&yp);
+    *       pp[s1]+=freq[s1][s2][iage] weighted
-   jprojmean=yp;
+    *       pos+=freq[s1][s2][iage] weighted
-   if(jprojmean==0) jprojmean=1;
+    *       Loop on s1 initial state
-   if(mprojmean==0) jprojmean=1;
+    *         fprintf(ficresp
+    *       end s1
-   i1=cptcoveff;
+    *     end age
-   if (cptcovn < 1){i1=1;}
+    *     if j!=0 computes starting values
+    *     end compute starting values
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+    *   end j1
+    * end nl
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+    */
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
- /*            if (h==(int)(YEARM*yearp)){ */
+     if(nj==1)
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+       j=0;  /* First pass for the constant */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     else{
-       k=k+1;
+       j=cptcoveff; /* Other passes for the covariate values */
-       fprintf(ficresf,"\n#******");
+     }
-       for(j=1;j<=cptcoveff;j++) {
+     first=1;
-         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]]);
+     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
-       }
+       posproptt=0.;
-       fprintf(ficresf,"******\n");
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+         scanf("%d", i);*/
-       for(j=1; j<=nlstate+ndeath;j++){
+       for (i=-5; i<=nlstate+ndeath; i++)
-         for(i=1; i<=nlstate;i++)
+         for (s2=-5; s2<=nlstate+ndeath; s2++)
-           fprintf(ficresf," p%d%d",i,j);
+           for(m=iagemin; m <= iagemax+3; m++)
-         fprintf(ficresf," p.%d",j);
+             freq[i][s2][m]=0;
-       }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       for (i=1; i<=nlstate; i++)  {
-         fprintf(ficresf,"\n");
+         for(m=iagemin; m <= iagemax+3; m++)
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+           prop[i][m]=0;
+         posprop[i]=0;
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+         pospropt[i]=0;
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       }
-           nhstepm = nhstepm/hstepm;
+       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         idq[z1]=0.;
-           oldm=oldms;savm=savms;
+         meanq[z1]=0.;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         stdq[z1]=0.;
+       }
-           for (h=0; h<=nhstepm; h++){
+       /* for (z1=1; z1<= nqtveff; z1++) { */
-             if (h*hstepm/YEARM*stepm ==yearp) {
+       /*   for(m=1;m<=lastpass;m++){ */
-               fprintf(ficresf,"\n");
+       /*          meanqt[m][z1]=0.; */
-               for(j=1;j<=cptcoveff;j++)
+       /*        } */
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       /* }       */
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+       /* dateintsum=0; */
-             }
+       /* k2cpt=0; */
-             for(j=1; j<=nlstate+ndeath;j++) {
-               ppij=0.;
+       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
-               for(i=1; i<=nlstate;i++) {
+       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-                 if (mobilav==1)
+         bool=1;
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+         if(j !=0){
-                 else {
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-                 }
+               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
-                 if (h*hstepm/YEARM*stepm== yearp) {
+                 /* if(Tvaraff[z1] ==-20){ */
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-                 }
+                 /* }else  if(Tvaraff[z1] ==-10){ */
-               } /* end i */
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-               if (h*hstepm/YEARM*stepm==yearp) {
+                 /* }else  */
-                 fprintf(ficresf," %.3f", ppij);
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
-               }
+                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
-             }/* end j */
+                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
-           } /* end h */
+                   /* 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",
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-         } /* end agec */
+                      j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-       } /* end yearp */
+                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-     } /* end cptcod */
+                 } /* Onlyf fixed */
-   } /* end  cptcov */
+               } /* end z1 */
+             } /* cptcovn > 0 */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           } /* end any */
+         }/* end j==0 */
-   fclose(ficresf);
+         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
- }
+           /* for(m=firstpass; m<=lastpass; m++){ */
+           for(mi=1; mi<wav[iind];mi++){ /* For each wave */
- /************** Forecasting *****not tested NB*************/
+             m=mw[mi][iind];
- 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){
+             if(j!=0){
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+                 for (z1=1; z1<=cptcoveff; z1++) {
-   int *popage;
+                   if( Fixed[Tmodelind[z1]]==1){
-   double calagedatem, agelim, kk1, kk2;
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-   double *popeffectif,*popcount;
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
-   double ***p3mat,***tabpop,***tabpopprev;
+                                                                                       value is -1, we don't select. It differs from the
-   double ***mobaverage;
+                                                                                       constant and age model which counts them. */
-   char filerespop[FILENAMELENGTH];
+                       bool=0; /* not selected */
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                       bool=0;
-   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);
+               }/* 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 */
-   strcpy(filerespop,"pop");
+             if(bool==1){ /*Selected */
-   strcat(filerespop,fileres);
+               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+                  and mw[mi+1][iind]. dh depends on stepm. */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-   }
+               if(m >=firstpass && m <=lastpass){
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+                 k2=anint[m][iind]+(mint[m][iind]/12.);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+                 /*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 (cptcoveff==0) ncodemax[cptcoveff]=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 */
-   if (mobilav!=0) {
+                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                 if (m<lastpass) {
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                   /*   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]); */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                   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 */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+                     idq[z1]=idq[z1]+weight[iind];
-   if (stepm<=12) stepsize=1;
+                     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 */
-   agelim=AGESUP;
+                   }
+                   /* if((int)agev[m][iind] == 55) */
-   hstepm=1;
+                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
-   hstepm=hstepm/stepm;
+                   /* 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 */
-   if (popforecast==1) {
+                 }
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+               } /* end if between passes */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+               if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+                 dateintsum=dateintsum+k2; /* on all covariates ?*/
-     }
+                 k2cpt++;
-     popage=ivector(0,AGESUP);
+                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-     popeffectif=vector(0,AGESUP);
+               }
-     popcount=vector(0,AGESUP);
+             }else{
+               bool=1;
-     i=1;
+             }/* end bool 2 */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+           } /* end m */
+           /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
-     imx=i;
+           /*   idq[z1]=idq[z1]+weight[iind]; */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+           /*   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 *\/ */
+           /* } */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+         } /* end bool */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       } /* end iind = 1 to imx */
-       k=k+1;
+       /* prop[s][age] is feeded for any initial and valid live state as well as
-       fprintf(ficrespop,"\n#******");
+          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       fprintf(ficrespop,"******\n");
+       if(cptcoveff==0 && nj==1) /* no covariate and first pass */
-       fprintf(ficrespop,"# Age");
+         pstamp(ficresp);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if  (cptcoveff>0 && j!=0){
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+         pstamp(ficresp);
+         printf( "\n#********** Variable ");
-       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficresp, "\n#********** Variable ");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+         fprintf(ficlog, "\n#********** Variable ");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+         for (z1=1; z1<=cptcoveff; z1++){
-           nhstepm = nhstepm/hstepm;
+           if(!FixedV[Tvaraff[z1]]){
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           oldm=oldms;savm=savms;
+             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           for (h=0; h<=nhstepm; h++){
+           }else{
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-             }
+             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-             for(j=1; j<=nlstate+ndeath;j++) {
+             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-               kk1=0.;kk2=0;
+             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-               for(i=1; i<=nlstate;i++) {
+           }
-                 if (mobilav==1)
+         }
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+         printf( "**********\n#");
-                 else {
+         fprintf(ficresp, "**********\n#");
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+         fprintf(ficresphtm, "**********</h3>\n");
-                 }
+         fprintf(ficresphtmfr, "**********</h3>\n");
-               }
+         fprintf(ficlog, "**********\n");
-               if (h==(int)(calagedatem+12*cpt)){
+       }
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+       /*
-                   /*fprintf(ficrespop," %.3f", kk1);
+         Printing means of quantitative variables if any
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+       */
-               }
+       for (z1=1; z1<= nqfveff; z1++) {
-             }
+         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
-             for(i=1; i<=nlstate;i++){
+         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
-               kk1=0.;
+         if(weightopt==1){
-                 for(j=1; j<=nlstate;j++){
+           printf(" Weighted mean and standard deviation of");
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+           fprintf(ficlog," Weighted mean and standard deviation of");
-                 }
+           fprintf(ficresphtmfr," Weighted mean and standard deviation of");
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+         }
-             }
+         printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+         fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+       }
-           }
+       /* for (z1=1; z1<= nqtveff; z1++) { */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /*        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\">");
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         fprintf(ficresp, " Age");
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       for(i=1; i<=nlstate;i++) {
-           nhstepm = nhstepm/hstepm;
+         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);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-           oldm=oldms;savm=savms;
+       if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fprintf(ficresphtm, "\n");
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       /* Header of frequency table by age */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-             }
+       fprintf(ficresphtmfr,"<th>Age</th> ");
-             for(j=1; j<=nlstate+ndeath;j++) {
+       for(s2=-1; s2 <=nlstate+ndeath; s2++){
-               kk1=0.;kk2=0;
+         for(m=-1; m <=nlstate+ndeath; m++){
-               for(i=1; i<=nlstate;i++) {
+           if(s2!=0 && m!=0)
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
-               }
+         }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+       }
-             }
+       fprintf(ficresphtmfr, "\n");
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* 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> ");
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         }else if(iage==iagemax+2){
+           fprintf(ficlog,"0");
-   if (popforecast==1) {
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-     free_ivector(popage,0,AGESUP);
+         }else if(iage==iagemax+3){
-     free_vector(popeffectif,0,AGESUP);
+           fprintf(ficlog,"Total");
-     free_vector(popcount,0,AGESUP);
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-   }
+         }else{
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           if(first==1){
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             first=0;
-   fclose(ficrespop);
+             printf("See log file for details...\n");
- } /* End of popforecast */
+           }
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
- int fileappend(FILE *fichier, char *optionfich)
+           fprintf(ficlog,"Age %d", iage);
- {
+         }
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+         for(s1=1; s1 <=nlstate ; s1++){
-     printf("Problem with file: %s\n", optionfich);
+           for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+             pp[s1] += freq[s1][m][iage];
-     return (0);
+         }
-   }
+         for(s1=1; s1 <=nlstate ; s1++){
-   fflush(fichier);
+           for(m=-1, pos=0; m <=0 ; m++)
-   return (1);
+             pos += freq[s1][m][iage];
- }
+           if(pp[s1]>=1.e-10){
+             if(first==1){
+               printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
- /**************** function prwizard **********************/
+             }
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
- {
+           }else{
+             if(first==1)
-   /* Wizard to print covariance matrix template */
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
-   char ca[32], cb[32], cc[32];
+           }
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+         }
-   int numlinepar;
+         for(s1=1; s1 <=nlstate ; s1++){
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           /* posprop[s1]=0; */
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-   for(i=1; i <=nlstate; i++){
+             pp[s1] += freq[s1][m][iage];
-     jj=0;
+         }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
-     for(j=1; j <=nlstate+ndeath; j++){
-       if(j==i) continue;
+         for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
-       jj++;
+           pos += pp[s1]; /* pos is the total number of transitions until this age */
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
-       printf("%1d%1d",i,j);
+                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-       fprintf(ficparo,"%1d%1d",i,j);
+           pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
-       for(k=1; k<=ncovmodel;k++){
+                                           from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-         /*        printf(" %lf",param[i][j][k]); */
+         }
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-         printf(" 0.");
+         /* Writing ficresp */
-         fprintf(ficparo," 0.");
+         if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
-       }
+           if( iage <= iagemax){
-       printf("\n");
+             fprintf(ficresp," %d",iage);
-       fprintf(ficparo,"\n");
+           }
-     }
+         }else if( nj==2){
-   }
+           if( iage <= iagemax){
-   printf("# Scales (for hessian or gradient estimation)\n");
+             fprintf(ficresp," %d",iage);
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+           }
-   for(i=1; i <=nlstate; i++){
+         }
-     jj=0;
+         for(s1=1; s1 <=nlstate ; s1++){
-     for(j=1; j <=nlstate+ndeath; j++){
+           if(pos>=1.e-5){
-       if(j==i) continue;
+             if(first==1)
-       jj++;
+               printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
-       fprintf(ficparo,"%1d%1d",i,j);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
-       printf("%1d%1d",i,j);
+           }else{
-       fflush(stdout);
+             if(first==1)
-       for(k=1; k<=ncovmodel;k++){
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
-         /*      printf(" %le",delti3[i][j][k]); */
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+           }
-         printf(" 0.");
+           if( iage <= iagemax){
-         fprintf(ficparo," 0.");
+             if(pos>=1.e-5){
-       }
+               if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
-       numlinepar++;
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
-       printf("\n");
+               }else if( nj==2){
-       fprintf(ficparo,"\n");
+                 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);
-   printf("# Covariance matrix\n");
+               /*probs[iage][s1][j1]= pp[s1]/pos;*/
- /* # 121 Var(a12)\n\ */
+               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+             } else{
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+               if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+             }
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+           }
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+           pospropt[s1] +=posprop[s1];
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+         } /* end loop s1 */
-   fflush(stdout);
+         /* pospropt=0.; */
-   fprintf(ficparo,"# Covariance matrix\n");
+         for(s1=-1; s1 <=nlstate+ndeath; s1++){
-   /* # 121 Var(a12)\n\ */
+           for(m=-1; m <=nlstate+ndeath; m++){
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+             if(freq[s1][m][iage] !=0 ) { /* minimizing output */
-   /* #   ...\n\ */
+               if(first==1){
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+                 printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
+               }
-   for(itimes=1;itimes<=2;itimes++){
+               /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
-     jj=0;
+               fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
-     for(i=1; i <=nlstate; i++){
+             }
-       for(j=1; j <=nlstate+ndeath; j++){
+             if(s1!=0 && m!=0)
-         if(j==i) continue;
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
-         for(k=1; k<=ncovmodel;k++){
+           }
-           jj++;
+         } /* end loop s1 */
-           ca[0]= k+'a'-1;ca[1]='\0';
+         posproptt=0.;
-           if(itimes==1){
+         for(s1=1; s1 <=nlstate; s1++){
-             printf("#%1d%1d%d",i,j,k);
+           posproptt += pospropt[s1];
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+         }
-           }else{
+         fprintf(ficresphtmfr,"</tr>\n ");
-             printf("%1d%1d%d",i,j,k);
+         fprintf(ficresphtm,"</tr>\n");
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+         if((cptcoveff==0 && nj==1)|| nj==2 ) {
-             /*  printf(" %.5le",matcov[i][j]); */
+           if(iage <= iagemax)
-           }
+             fprintf(ficresp,"\n");
-           ll=0;
+         }
-           for(li=1;li <=nlstate; li++){
+         if(first==1)
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+           printf("Others in log...\n");
-               if(lj==li) continue;
+         fprintf(ficlog,"\n");
-               for(lk=1;lk<=ncovmodel;lk++){
+       } /* end loop age iage */
-                 ll++;
-                 if(ll<=jj){
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+       for(s1=1; s1 <=nlstate ; s1++){
-                   if(ll<jj){
+         if(posproptt < 1.e-5){
-                     if(itimes==1){
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         }else{
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
-                     }else{
+         }
-                       printf(" 0.");
+       }
-                       fprintf(ficparo," 0.");
+       fprintf(ficresphtm,"</tr>\n");
-                     }
+       fprintf(ficresphtm,"</table>\n");
-                   }else{
+       fprintf(ficresphtmfr,"</table>\n");
-                     if(itimes==1){
+       if(posproptt < 1.e-5){
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-                     }else{
+         fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
-                       printf(" 0.");
+         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
-                       fprintf(ficparo," 0.");
+         invalidvarcomb[j1]=1;
-                     }
+       }else{
-                   }
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-                 }
+         invalidvarcomb[j1]=0;
-               } /* end lk */
+       }
-             } /* end lj */
+       fprintf(ficresphtmfr,"</table>\n");
-           } /* end li */
+       fprintf(ficlog,"\n");
-           printf("\n");
+       if(j!=0){
-           fprintf(ficparo,"\n");
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-           numlinepar++;
+         for(i=1,s1=1; i <=nlstate; i++){
-         } /* end k*/
+           for(k=1; k <=(nlstate+ndeath); k++){
-       } /*end j */
+             if (k != i) {
-     } /* end i */
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
-   } /* end itimes */
+                 if(jj==1){  /* Constant case (in fact cste + age) */
+                   if(j1==1){ /* All dummy covariates to zero */
- } /* end of prwizard */
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
- /******************* Gompertz Likelihood ******************************/
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
- double gompertz(double x[])
+                     printf("%d%d ",i,k);
- {
+                     fprintf(ficlog,"%d%d ",i,k);
-   double A,B,L=0.0,sump=0.,num=0.;
+                     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]));
-   int i,n=0; /* n is the size of the sample */
+                     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]);
-   for (i=0;i<=imx-1 ; i++) {
+                   }
-     sump=sump+weight[i];
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
-     /*    sump=sump+1;*/
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
-     num=num+1;
+                     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]); */
+                   }
-   /* for (i=0; i<=imx; i++)
+                   /* Some are not finite, but linreg will ignore these ages */
-      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]);*/
+                   no=0;
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
-   for (i=1;i<=imx ; i++)
+                   pstart[s1]=b;
-     {
+                   pstart[s1-1]=a;
-       if (cens[i] == 1 && wav[i]>1)
+                 }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 */
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+                   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]);
-       if (cens[i] == 0 && wav[i]>1)
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+                   printf("%d%d ",i,k);
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+                   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]));
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
-       if (wav[i] > 1 ) { /* ??? */
+                   ;
-         L=L+A*weight[i];
+                 }
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+                 /* printf("%12.7f )", param[i][jj][k]); */
-       }
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
-     }
+                 s1++;
+               } /* end jj */
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+             } /* end k!= i */
+           } /* end k */
-   return -2*L*num/sump;
+         } /* end i, s1 */
- }
+       } /* end j !=0 */
+     } /* end selected combination of covariate j1 */
- /******************* Printing html file ***********/
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+       printf("#Freqsummary: Starting values for the constants:\n");
-                   int lastpass, int stepm, int weightopt, char model[],\
+       fprintf(ficlog,"\n");
-                   int imx,  double p[],double **matcov,double agemortsup){
+       for(i=1,s1=1; i <=nlstate; i++){
-   int i,k;
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+             printf("%d%d ",i,k);
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+             fprintf(ficlog,"%d%d ",i,k);
-   for (i=1;i<=2;i++)
+             for(jj=1; jj <=ncovmodel; jj++){
-     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]));
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+               if(jj==1){ /* Age has to be done */
-   fprintf(fichtm,"</ul>");
+                 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(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+                 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]));
+               }
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+               /* printf("%12.7f )", param[i][jj][k]); */
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
-  for (k=agegomp;k<(agemortsup-2);k++)
+               s1++;
-    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
-   fflush(fichtm);
+           }
- }
+         }
+       } /* end of state i */
- /******************* Gnuplot file **************/
+       printf("#Freqsummary\n");
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+       fprintf(ficlog,"\n");
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
-   char dirfileres[132],optfileres[132];
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
-   int ng;
+           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 *\/ */
-   /*#ifdef windows */
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
-     /*#endif */
+           /* } */
+         }
+       } /* end loop s1 */
-   strcpy(dirfileres,optionfilefiname);
-   strcpy(optfileres,"vpl");
+       printf("\n");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+       fprintf(ficlog,"\n");
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+     } /* end j=0 */
-   fprintf(ficgp, "set ter png small\n set log y\n");
+   } /* end j */
-   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);
+   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]); */
- /**************** Main Program *****************/
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
- /***********************************************/
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
- int main(int argc, char *argv[])
+             fprintf(ficparo," %f ",pstart[jk]);
- {
+             jk++;
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+           }
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+           printf("\n");
-   int linei, month, year,iout;
+           fprintf(ficparo,"\n");
-   int jj, ll, li, lj, lk, imk;
+         }
-   int numlinepar=0; /* Current linenumber of parameter file */
+       }
-   int itimes;
+     }
-   int NDIM=2;
+   } /* end mle=-2 */
+   dateintmean=dateintsum/k2cpt;
-   char ca[32], cb[32], cc[32];
-   char dummy[]="                         ";
+   fclose(ficresp);
-   /*  FILE *fichtm; *//* Html File */
+   fclose(ficresphtm);
-   /* FILE *ficgp;*/ /*Gnuplot File */
+   fclose(ficresphtmfr);
-   struct stat info;
+   free_vector(idq,1,nqfveff);
-   double agedeb, agefin,hf;
+   free_vector(meanq,1,nqfveff);
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   free_vector(stdq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
-   double fret;
+   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
-   double **xi,tmp,delta;
+   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
-   double dum; /* Dummy variable */
+   free_vector(pospropt,1,nlstate);
-   double ***p3mat;
+   free_vector(posprop,1,nlstate);
-   double ***mobaverage;
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
-   int *indx;
+   free_vector(pp,1,nlstate);
-   char line[MAXLINE], linepar[MAXLINE];
+   /* End of freqsummary */
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+ }
-   char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+ /* Simple linear regression */
-   int firstobs=1, lastobs=10;
+ int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
+   /* y=a+bx regression */
-   int ju,jl, mi;
+   double   sumx = 0.0;                        /* sum of x                      */
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   double   sumx2 = 0.0;                       /* sum of x**2                   */
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   double   sumxy = 0.0;                       /* sum of x * y                  */
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   double   sumy = 0.0;                        /* sum of y                      */
-   int mobilav=0,popforecast=0;
+   double   sumy2 = 0.0;                       /* sum of y**2                   */
-   int hstepm, nhstepm;
+   double   sume2 = 0.0;                       /* sum of square or residuals */
-   int agemortsup;
+   double yhat;
-   float  sumlpop=0.;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   double denom=0;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   int i;
+   int ne=*no;
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
+   for ( i=ifi, ne=0;i<=ila;i++) {
-   double **prlim;
+     if(!isfinite(x[i]) || !isfinite(y[i])){
-   double *severity;
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
-   double ***param; /* Matrix of parameters */
+       continue;
-   double  *p;
+     }
-   double **matcov; /* Matrix of covariance */
+     ne=ne+1;
-   double ***delti3; /* Scale */
+     sumx  += x[i];
-   double *delti; /* Scale */
+     sumx2 += x[i]*x[i];
-   double ***eij, ***vareij;
+     sumxy += x[i] * y[i];
-   double **varpl; /* Variances of prevalence limits by age */
+     sumy  += y[i];
-   double *epj, vepp;
+     sumy2 += y[i]*y[i];
-   double kk1, kk2;
+     denom = (ne * sumx2 - sumx*sumx);
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+     /* 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); */
-   double **ximort;
+   }
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
-   int *dcwave;
+   denom = (ne * sumx2 - sumx*sumx);
+   if (denom == 0) {
-   char z[1]="c", occ;
+     // vertical, slope m is infinity
+     *b = INFINITY;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+     *a = 0;
-   char  *strt, strtend[80];
+     if (r) *r = 0;
-   char *stratrunc;
+     return 1;
-   int lstra;
+   }
-   long total_usecs;
+   *b = (ne * sumxy  -  sumx * sumy) / denom;
+   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
- /*   setlocale (LC_ALL, ""); */
+   if (r!=NULL) {
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
- /*   textdomain (PACKAGE); */
+       sqrt((sumx2 - sumx*sumx/ne) *
- /*   setlocale (LC_CTYPE, ""); */
+            (sumy2 - sumy*sumy/ne));
- /*   setlocale (LC_MESSAGES, ""); */
+   }
+   *no=ne;
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   for ( i=ifi, ne=0;i<=ila;i++) {
-   (void) gettimeofday(&start_time,&tzp);
+     if(!isfinite(x[i]) || !isfinite(y[i])){
-   curr_time=start_time;
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
-   tm = *localtime(&start_time.tv_sec);
+       continue;
-   tmg = *gmtime(&start_time.tv_sec);
+     }
-   strcpy(strstart,asctime(&tm));
+     ne=ne+1;
+     yhat = y[i] - *a -*b* x[i];
- /*  printf("Localtime (at start)=%s",strstart); */
+     sume2  += yhat * yhat ;
- /*  tp.tv_sec = tp.tv_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+     denom = (ne * sumx2 - sumx*sumx);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+     /* 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); */
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+   }
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
- /*   tp.tv_sec = mktime(&tmg); */
+   *sa= *sb * sqrt(sumx2/ne);
- /*   strt=asctime(&tmg); */
- /*   printf("Time(after) =%s",strstart);  */
+   return 0;
- /*  (void) time (&time_value);
+ }
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
- *  tm = *localtime(&time_value);
+ /************ Prevalence ********************/
- *  strstart=asctime(&tm);
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ {
- */
+   /* 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).
-   nberr=0; /* Number of errors and warnings */
+      We still use firstpass and lastpass as another selection.
-   nbwarn=0;
+   */
-   getcwd(pathcd, size);
+   int i, m, jk, j1, bool, z1,j, iv;
-   printf("\n%s\n%s",version,fullversion);
+   int mi; /* Effective wave */
-   if(argc <=1){
+   int iage;
-     printf("\nEnter the parameter file name: ");
+   double agebegin, ageend;
-     fgets(pathr,FILENAMELENGTH,stdin);
-     i=strlen(pathr);
+   double **prop;
-     if(pathr[i-1]=='\n')
+   double posprop;
-       pathr[i-1]='\0';
+   double  y2; /* in fractional years */
-    for (tok = pathr; tok != NULL; ){
+   int iagemin, iagemax;
-       printf("Pathr |%s|\n",pathr);
+   int first; /** to stop verbosity which is redirected to log file */
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-       printf("val= |%s| pathr=%s\n",val,pathr);
+   iagemin= (int) agemin;
-       strcpy (pathtot, val);
+   iagemax= (int) agemax;
-       if(pathr[0] == '\0') break; /* Dirty */
+   /*pp=vector(1,nlstate);*/
-     }
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
-   }
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   else{
+   j1=0;
-     strcpy(pathtot,argv[1]);
-   }
+   /*j=cptcoveff;*/
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   /*cygwin_split_path(pathtot,path,optionfile);
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   first=0;
-   /* cutv(path,optionfile,pathtot,'\\');*/
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
+     for (i=1; i<=nlstate; i++)
-   /* Split argv[0], imach program to get pathimach */
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+         prop[i][iage]=0.0;
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
-  /*   strcpy(pathimach,argv[0]); */
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+     for (i=1; i<=imx; i++) { /* Each individual */
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+       bool=1;
-   chdir(path); /* Can be a relative path */
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-     printf("Current directory %s!\n",pathcd);
+         m=mw[mi][i];
-   strcpy(command,"mkdir ");
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
-   strcat(command,optionfilefiname);
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
-   if((outcmd=system(command)) != 0){
+         for (z1=1; z1<=cptcoveff; z1++){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+           if( Fixed[Tmodelind[z1]]==1){
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-     /* fclose(ficlog); */
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
- /*     exit(1); */
+               bool=0;
-   }
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
- /*     perror("mkdir"); */
+               bool=0;
- /*   } */
+             }
+         }
-   /*-------- arguments in the command line --------*/
+         if(bool==1){ /* Otherwise we skip that wave/person */
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-   /* Log file */
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-   strcat(filelog, optionfilefiname);
+           if(m >=firstpass && m <=lastpass){
-   strcat(filelog,".log");    /* */
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-     printf("Problem with logfile %s\n",filelog);
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-     goto end;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-   }
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+                 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);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+                 exit(1);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+               }
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-  path=%s \n\
+                 /*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]]);*/
-  optionfile=%s\n\
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
-  optionfilext=%s\n\
+                 prop[s[m][i]][iagemax+3] += weight[i];
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+               } /* end valid statuses */
+             } /* end selection of dates */
-   printf("Local time (at start):%s",strstart);
+           } /* end selection of waves */
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+         } /* end bool */
-   fflush(ficlog);
+       } /* end wave */
- /*   (void) gettimeofday(&curr_time,&tzp); */
+     } /* end individual */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+     for(i=iagemin; i <= iagemax+3; i++){
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   /* */
+         posprop += prop[jk][i];
-   strcpy(fileres,"r");
+       }
-   strcat(fileres, optionfilefiname);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+       for(jk=1; jk <=nlstate ; jk++){
+         if( i <=  iagemax){
-   /*---------arguments file --------*/
+           if(posprop>=1.e-5){
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+           } else{
-     printf("Problem with optionfile %s\n",optionfile);
+             if(!first){
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+               first=1;
-     fflush(ficlog);
+               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]);
-     goto end;
+             }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]);
+             }
+           }
+         }
-   strcpy(filereso,"o");
+       }/* end jk */
-   strcat(filereso,fileres);
+     }/* end i */
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+      /*} *//* end i1 */
-     printf("Problem with Output resultfile: %s\n", filereso);
+   } /* end j1 */
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-     fflush(ficlog);
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-     goto end;
+   /*free_vector(pp,1,nlstate);*/
-   }
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+ }  /* End of prevalence */
-   /* Reads comments: lines beginning with '#' */
-   numlinepar=0;
+ /************* Waves Concatenation ***************/
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+ 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)
-     fgets(line, MAXLINE, ficpar);
+ {
-     numlinepar++;
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-     puts(line);
+      Death is a valid wave (if date is known).
-     fputs(line,ficparo);
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-     fputs(line,ficlog);
+      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.
-   ungetc(c,ficpar);
+   */
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   int i=0, mi=0, m=0, mli=0;
-   numlinepar++;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   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);
+      double sum=0., jmean=0.;*/
-   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);
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
-   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);
+   int j, k=0,jk, ju, jl;
-   fflush(ficlog);
+   double sum=0.;
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   first=0;
-     ungetc(c,ficpar);
+   firstwo=0;
-     fgets(line, MAXLINE, ficpar);
+   firsthree=0;
-     numlinepar++;
+   firstfour=0;
-     puts(line);
+   jmin=100000;
-     fputs(line,ficparo);
+   jmax=-1;
-     fputs(line,ficlog);
+   jmean=0.;
-   }
-   ungetc(c,ficpar);
+ /* Treating live states */
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
+     mi=0;  /* First valid wave */
-   covar=matrix(0,NCOVMAX,1,n);
+     mli=0; /* Last valid wave */
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+     m=firstpass;
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+     while(s[m][i] <= nlstate){  /* a live 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 */
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+         mli=m-1;/* mw[++mi][i]=m-1; */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       }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 */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         mw[++mi][i]=m;
+         mli=m;
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
-   delti=delti3[1][1];
+       if(m < lastpass){ /* m < lastpass, standard case */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+       }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+       else{ /* m >= lastpass, eventual special issue with warning */
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+         break;
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ #else
-     fclose (ficparo);
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
-     fclose (ficlog);
+           if(firsthree == 0){
-     goto end;
+             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);
-     exit(0);
+             firsthree=1;
-   }
+           }
-   else if(mle==-3) {
+           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);
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+           mw[++mi][i]=m;
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+           mli=m;
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+         }
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         if(s[m][i]==-2){ /* Vital status is really unknown */
-     matcov=matrix(1,npar,1,npar);
+           nbwarn++;
-   }
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
-   else{
+             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);
-     /* Read guess parameters */
+             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);
-     /* Reads comments: lines beginning with '#' */
+           }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           break;
-       ungetc(c,ficpar);
+         }
-       fgets(line, MAXLINE, ficpar);
+         break;
-       numlinepar++;
+ #endif
-       puts(line);
+       }/* End m >= lastpass */
-       fputs(line,ficparo);
+     }/* end while */
-       fputs(line,ficlog);
-     }
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
-     ungetc(c,ficpar);
+     /* After last pass */
+ /* Treating death states */
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     if (s[m][i] > nlstate){  /* In a death state */
-     for(i=1; i <=nlstate; i++){
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
-       j=0;
+       /* } */
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+       mi++;     /* Death is another wave */
-         if(jj==i) continue;
+       /* if(mi==0)  never been interviewed correctly before death */
-         j++;
+       /* Only death is a correct wave */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       mw[mi][i]=m;
-         if ((i1 != i) && (j1 != j)){
+     } /* else not in a death state */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
- It might be a problem of design; if ncovcol and the model are correct\n \
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-           exit(1);
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
-         }
+           nbwarn++;
-         fprintf(ficparo,"%1d%1d",i1,j1);
+           if(firstfiv==0){
-         if(mle==1)
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
-           printf("%1d%1d",i,j);
+             firstfiv=1;
-         fprintf(ficlog,"%1d%1d",i,j);
+           }else{
-         for(k=1; k<=ncovmodel;k++){
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
-           fscanf(ficpar," %lf",&param[i][j][k]);
+           }
-           if(mle==1){
+         }else{ /* Death occured afer last wave potential bias */
-             printf(" %lf",param[i][j][k]);
+           nberr++;
-             fprintf(ficlog," %lf",param[i][j][k]);
+           if(firstwo==0){
-           }
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). 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], i,m );
-           else
+             firstwo=1;
-             fprintf(ficlog," %lf",param[i][j][k]);
+           }
-           fprintf(ficparo," %lf",param[i][j][k]);
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
          }
-         fscanf(ficpar,"\n");
+       }else{ /* if date of interview is unknown */
-         numlinepar++;
+         /* death is known but not confirmed by death status at any wave */
-         if(mle==1)
+         if(firstfour==0){
-           printf("\n");
+           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. 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], i,m );
-         fprintf(ficlog,"\n");
+           firstfour=1;
-         fprintf(ficparo,"\n");
+         }
-       }
+         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. 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], i,m );
-     }
+       }
-     fflush(ficlog);
+     } /* end if date of death is known */
+ #endif
-     p=param[1][1];
+     wav[i]=mi; /* mi should be the last effective wave (or mli) */
+     /* wav[i]=mw[mi][i]; */
-     /* Reads comments: lines beginning with '#' */
+     if(mi==0){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       nbwarn++;
-       ungetc(c,ficpar);
+       if(first==0){
-       fgets(line, MAXLINE, ficpar);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-       numlinepar++;
+         first=1;
-       puts(line);
+       }
-       fputs(line,ficparo);
+       if(first==1){
-       fputs(line,ficlog);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-     }
+       }
-     ungetc(c,ficpar);
+     } /* end mi==0 */
+   } /* End individuals */
-     for(i=1; i <=nlstate; i++){
+   /* wav and mw are no more changed */
-       for(j=1; j <=nlstate+ndeath-1; j++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+   for(i=1; i<=imx; i++){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+     for(mi=1; mi<wav[i];mi++){
-           exit(1);
+       if (stepm <=0)
-         }
+         dh[mi][i]=1;
-         printf("%1d%1d",i,j);
+       else{
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
-         fprintf(ficlog,"%1d%1d",i1,j1);
+           if (agedc[i] < 2*AGESUP) {
-         for(k=1; k<=ncovmodel;k++){
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           printf(" %le",delti3[i][j][k]);
+             else if(j<0){
-           fprintf(ficparo," %le",delti3[i][j][k]);
+               nberr++;
-           fprintf(ficlog," %le",delti3[i][j][k]);
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         }
+               j=1; /* Temporary Dangerous patch */
-         fscanf(ficpar,"\n");
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-         numlinepar++;
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         printf("\n");
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-         fprintf(ficparo,"\n");
+             }
-         fprintf(ficlog,"\n");
+             k=k+1;
-       }
+             if (j >= jmax){
-     }
+               jmax=j;
-     fflush(ficlog);
+               ijmax=i;
+             }
-     delti=delti3[1][1];
+             if (j <= jmin){
+               jmin=j;
+               ijmin=i;
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+             }
+             sum=sum+j;
-     /* Reads comments: lines beginning with '#' */
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-     while((c=getc(ficpar))=='#' && c!= EOF){
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-       ungetc(c,ficpar);
+           }
-       fgets(line, MAXLINE, ficpar);
+         }
-       numlinepar++;
+         else{
-       puts(line);
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-       fputs(line,ficparo);
+ /*        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]); */
-       fputs(line,ficlog);
-     }
+           k=k+1;
-     ungetc(c,ficpar);
+           if (j >= jmax) {
+             jmax=j;
-     matcov=matrix(1,npar,1,npar);
+             ijmax=i;
-     for(i=1; i <=npar; i++){
+           }
-       fscanf(ficpar,"%s",&str);
+           else if (j <= jmin){
-       if(mle==1)
+             jmin=j;
-         printf("%s",str);
+             ijmin=i;
-       fprintf(ficlog,"%s",str);
+           }
-       fprintf(ficparo,"%s",str);
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-       for(j=1; j <=i; j++){
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-         fscanf(ficpar," %le",&matcov[i][j]);
+           if(j<0){
-         if(mle==1){
+             nberr++;
-           printf(" %.5le",matcov[i][j]);
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         }
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         fprintf(ficlog," %.5le",matcov[i][j]);
+           }
-         fprintf(ficparo," %.5le",matcov[i][j]);
+           sum=sum+j;
-       }
+         }
-       fscanf(ficpar,"\n");
+         jk= j/stepm;
-       numlinepar++;
+         jl= j -jk*stepm;
-       if(mle==1)
+         ju= j -(jk+1)*stepm;
-         printf("\n");
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-       fprintf(ficlog,"\n");
+           if(jl==0){
-       fprintf(ficparo,"\n");
+             dh[mi][i]=jk;
-     }
+             bh[mi][i]=0;
-     for(i=1; i <=npar; i++)
+           }else{ /* We want a negative bias in order to only have interpolation ie
-       for(j=i+1;j<=npar;j++)
+                   * to avoid the price of an extra matrix product in likelihood */
-         matcov[i][j]=matcov[j][i];
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
-     if(mle==1)
+           }
-       printf("\n");
+         }else{
-     fprintf(ficlog,"\n");
+           if(jl <= -ju){
+             dh[mi][i]=jk;
-     fflush(ficlog);
+             bh[mi][i]=jl;       /* bias is positive if real duration
+                                  * is higher than the multiple of stepm and negative otherwise.
-     /*-------- Rewriting parameter file ----------*/
+                                  */
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+           }
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+           else{
-     strcat(rfileres,".");    /* */
+             dh[mi][i]=jk+1;
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+             bh[mi][i]=ju;
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+           }
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+           if(dh[mi][i]==0){
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+             dh[mi][i]=1; /* At least one step */
-     }
+             bh[mi][i]=ju; /* At least one step */
-     fprintf(ficres,"#%s\n",version);
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-   }    /* End of mle != -3 */
+           }
+         } /* end if mle */
-   /*-------- data file ----------*/
+       }
-   if((fic=fopen(datafile,"r"))==NULL)    {
+     } /* end wave */
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+   }
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   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);
-   n= lastobs;
+ }
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
+ /*********** Tricode ****************************/
-   num=lvector(1,n);
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
-   moisnais=vector(1,n);
+  {
-   annais=vector(1,n);
+    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   moisdc=vector(1,n);
+    /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   andc=vector(1,n);
+     * Boring subroutine which should only output nbcode[Tvar[j]][k]
-   agedc=vector(1,n);
+     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-   cod=ivector(1,n);
+     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
-   weight=vector(1,n);
+     */
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-   mint=matrix(1,maxwav,1,n);
+    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   anint=matrix(1,maxwav,1,n);
+    int modmaxcovj=0; /* Modality max of covariates j */
-   s=imatrix(1,maxwav+1,1,n);
+    int cptcode=0; /* Modality max of covariates j */
-   tab=ivector(1,NCOVMAX);
+    int modmincovj=0; /* Modality min of covariates j */
-   ncodemax=ivector(1,8);
-   i=1;
+    /* cptcoveff=0;  */
-   linei=0;
+    /* *cptcov=0; */
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     linei=linei+1;
+    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+    for (k=1; k <= maxncov; k++)
-       if(line[j] == '\t')
+      for(j=1; j<=2; j++)
-         line[j] = ' ';
+        nbcode[k][j]=0; /* Valgrind */
-     }
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+    /* Loop on covariates without age and products and no quantitative variable */
-       ;
+    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     };
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-     line[j+1]=0;  /* Trims blanks at end of line */
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-     if(line[0]=='#'){
+        switch(Fixed[k]) {
-       fprintf(ficlog,"Comment line\n%s\n",line);
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-       printf("Comment line\n%s\n",line);
+          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*/
-       continue;
+            ij=(int)(covar[Tvar[k]][i]);
-     }
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+             * If product of Vn*Vm, still boolean *:
-     for (j=maxwav;j>=1;j--){
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-       cutv(stra, strb,line,' ');
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-       errno=0;
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       lval=strtol(strb,&endptr,10);
+               modality of the nth covariate of individual i. */
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+            if (ij > modmaxcovj)
-       if( strb[0]=='\0' || (*endptr != '\0')){
+              modmaxcovj=ij;
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+            else if (ij < modmincovj)
-         exit(1);
+              modmincovj=ij;
-       }
+            if (ij <0 || ij >1 ){
-       s[j][i]=lval;
+              printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
+              fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
-       strcpy(line,stra);
+            }
-       cutv(stra, strb,line,' ');
+            if ((ij < -1) || (ij > NCOVMAX)){
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-       }
+              exit(1);
-       else  if(iout=sscanf(strb,"%s.") != 0){
+            }else
-         month=99;
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-         year=9999;
+            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-       }else{
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+            /* getting the maximum value of the modality of the covariate
-         exit(1);
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-       }
+               female ies 1, then modmaxcovj=1.
-       anint[j][i]= (double) year;
+            */
-       mint[j][i]= (double)month;
+          } /* end for loop on individuals i */
-       strcpy(line,stra);
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-     } /* ENd Waves */
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+          cptcode=modmaxcovj;
-     cutv(stra, strb,line,' ');
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+          /*for (i=0; i<=cptcode; i++) {*/
-     }
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-       month=99;
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-       year=9999;
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-     }else{
+              if( j != -1){
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-       exit(1);
+                                   covariate for which somebody answered excluding
-     }
+                                   undefined. Usually 2: 0 and 1. */
-     andc[i]=(double) year;
+              }
-     moisdc[i]=(double) month;
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
-     strcpy(line,stra);
+                                      covariate for which somebody answered including
+                                      undefined. Usually 3: -1, 0 and 1. */
-     cutv(stra, strb,line,' ');
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-     }
+          } /* Ndum[-1] number of undefined modalities */
-     else  if(iout=sscanf(strb,"%s.") != 0){
-       month=99;
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-       year=9999;
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-     }else{
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+          /* modmincovj=3; modmaxcovj = 7; */
-       exit(1);
+          /* 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; */
-     annais[i]=(double)(year);
+          /*              defining two dummy variables: variables V1_1 and V1_2.*/
-     moisnais[i]=(double)(month);
+          /* nbcode[Tvar[j]][ij]=k; */
-     strcpy(line,stra);
+          /* nbcode[Tvar[j]][1]=0; */
+          /* nbcode[Tvar[j]][2]=1; */
-     cutv(stra, strb,line,' ');
+          /* nbcode[Tvar[j]][3]=2; */
-     errno=0;
+          /* To be continued (not working yet). */
-     dval=strtod(strb,&endptr);
+          ij=0; /* ij is similar to i but can jump over null modalities */
-     if( strb[0]=='\0' || (*endptr != '\0')){
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+          /* 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*/
-       exit(1);
+          /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
-     }
+          /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
-     weight[i]=dval;
+           * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
-     strcpy(line,stra);
+          /*, could be restored in the future */
+          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*/
-     for (j=ncovcol;j>=1;j--){
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-       cutv(stra, strb,line,' ');
+              break;
-       errno=0;
+            }
-       lval=strtol(strb,&endptr,10);
+            ij++;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+            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*/
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+            cptcode = ij; /* New max modality for covar j */
-         exit(1);
+          } /* end of loop on modality i=-1 to 1 or more */
-       }
+          break;
-       if(lval <-1 || lval >1){
+        case 1: /* Testing on varying covariate, could be simple and
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+                 * should look at waves or product of fixed *
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+                 * varying. No time to test -1, assuming 0 and 1 only */
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+          ij=0;
-  For example, for multinomial values like 1, 2 and 3,\n \
+          for(i=0; i<=1;i++){
-  build V1=0 V2=0 for the reference value (1),\n \
+            nbcode[Tvar[k]][++ij]=i;
-         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 \
+          break;
-  output of IMaCh is often meaningless.\n \
+        default:
-  Exiting.\n",lval,linei, i,line,j);
+          break;
-         exit(1);
+        } /* end switch */
-       }
+      } /* end dummy test */
-       covar[j][i]=(double)(lval);
+    } /* 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*/
-       strcpy(line,stra);
-     }
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
-     lstra=strlen(stra);
+    /* 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 */
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-       stratrunc = &(stra[lstra-9]);
+      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 */
-       num[i]=atol(stratrunc);
+      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} */
-     else
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-       num[i]=atol(stra);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+    ij=0;
-       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+    /* 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++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     i=i+1;
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   } /* End loop reading  data */
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-   fclose(fic);
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-   /* printf("ii=%d", ij);
+        /* If product not in single variable we don't print results */
-      scanf("%d",i);*/
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   imx=i-1; /* Number of individuals */
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+        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*/
-   /* for (i=1; i<=imx; i++){
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+        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 ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+        if(Fixed[k]!=0)
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+          anyvaryingduminmodel=1;
-     }*/
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
-    /*  for (i=1; i<=imx; i++){
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
-      if (s[4][i]==9)  s[4][i]=-1;
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
-   /* for (i=1; i<=imx; i++) */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+      }
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
-      else weight[i]=1;*/
+    /* ij--; */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
-   /* Calculation of the number of parameters from char model */
+    *cptcov=ij; /*Number of total real effective covariates: effective
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+                 * because they can be excluded from the model and real
-   Tprod=ivector(1,15);
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
-   Tvaraff=ivector(1,15);
+    for(j=ij+1; j<= cptcovt; j++){
-   Tvard=imatrix(1,15,1,2);
+      Tvaraff[j]=0;
-   Tage=ivector(1,15);
+      Tmodelind[j]=0;
+    }
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+    for(j=ntveff+1; j<= cptcovt; j++){
-     j=0, j1=0, k1=1, k2=1;
+      TmodelInvind[j]=0;
-     j=nbocc(model,'+'); /* j=Number of '+' */
+    }
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+    /* To be sorted */
-     cptcovn=j+1;
+    ;
-     cptcovprod=j1; /*Number of products */
+  }
-     strcpy(modelsav,model);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+ /*********** Health Expectancies ****************/
-       printf("Error. Non available option model=%s ",model);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+  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 )
-       goto end;
-     }
+ {
+   /* Health expectancies, no variances */
-     /* This loop fills the array Tvar from the string 'model'.*/
+   int i, j, nhstepm, hstepm, h, nstepm;
+   int nhstepma, nstepma; /* Decreasing with age */
-     for(i=(j+1); i>=1;i--){
+   double age, agelim, hf;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+   double ***p3mat;
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   double eip;
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-       /*scanf("%d",i);*/
+   /* pstamp(ficreseij); */
-       if (strchr(strb,'*')) {  /* Model includes a product */
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+   fprintf(ficreseij,"# Age");
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+   for(i=1; i<=nlstate;i++){
-           cptcovprod--;
+     for(j=1; j<=nlstate;j++){
-           cutv(strb,stre,strd,'V');
+       fprintf(ficreseij," e%1d%1d ",i,j);
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+     }
-           cptcovage++;
+     fprintf(ficreseij," e%1d. ",i);
-             Tage[cptcovage]=i;
+   }
-             /*printf("stre=%s ", stre);*/
+   fprintf(ficreseij,"\n");
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+   if(estepm < stepm){
-           cutv(strb,stre,strc,'V');
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-           Tvar[i]=atoi(stre);
+   }
-           cptcovage++;
+   else  hstepm=estepm;
-           Tage[cptcovage]=i;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-         }
+    * This is mainly to measure the difference between two models: for example
-         else {  /* Age is not in the model */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-           Tvar[i]=ncovcol+k1;
+    * progression in between and thus overestimating or underestimating according
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+    * to the curvature of the survival function. If, for the same date, we
-           Tprod[k1]=i;
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-           Tvard[k1][1]=atoi(strc); /* m*/
+    * to compare the new estimate of Life expectancy with the same linear
-           Tvard[k1][2]=atoi(stre); /* n */
+    * hypothesis. A more precise result, taking into account a more precise
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+    * curvature will be obtained if estepm is as small as stepm. */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
-           for (k=1; k<=lastobs;k++)
+   /* For example we decided to compute the life expectancy with the smallest unit */
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-           k1++;
+      nhstepm is the number of hstepm from age to agelim
-           k2=k2+2;
+      nstepm is the number of stepm from age to agelin.
-         }
+      Look at hpijx to understand the reason which relies in memory size consideration
-       }
+      and note for a fixed period like estepm months */
-       else { /* no more sum */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+      survival function given by stepm (the optimization length). Unfortunately it
-        /*  scanf("%d",i);*/
+      means that if the survival funtion is printed only each two years of age and if
-       cutv(strd,strc,strb,'V');
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-       Tvar[i]=atoi(strc);
+      results. So we changed our mind and took the option of the best precision.
-       }
+   */
-       strcpy(modelsav,stra);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-         scanf("%d",i);*/
+   agelim=AGESUP;
-     } /* end of loop + */
+   /* If stepm=6 months */
-   } /* end model */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-   /*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*/
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   printf("cptcovprod=%d ", cptcovprod);
+   /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   scanf("%d ",i);*/
+   for (age=bage; age<=fage; age ++){
-     /*  if(mle==1){*/
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   if (weightopt != 1) { /* Maximisation without weights*/
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     for(i=1;i<=n;i++) weight[i]=1.0;
+     /* if (stepm >= YEARM) hstepm=1;*/
-   }
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     /*-calculation of age at interview from date of interview and age at death -*/
-   agev=matrix(1,maxwav,1,imx);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   for (i=1; i<=imx; i++) {
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     for(m=2; (m<= maxwav); m++) {
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
-         anint[m][i]=9999;
-         s[m][i]=-1;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+     printf("%d|",(int)age);fflush(stdout);
-         nberr++;
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+     /* Computing expectancies */
-         s[m][i]=-1;
+     for(i=1; i<=nlstate;i++)
-       }
+       for(j=1; j<=nlstate;j++)
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-         nberr++;
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+           /* 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]);*/
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       }
+         }
-     }
-   }
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-   for (i=1; i<=imx; i++)  {
+       eip=0;
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+       for(j=1; j<=nlstate;j++){
-     for(m=firstpass; (m<= lastpass); m++){
+         eip +=eij[i][j][(int)age];
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-         if (s[m][i] >= nlstate+1) {
+       }
-           if(agedc[i]>0)
+       fprintf(ficreseij,"%9.4f", eip );
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     }
-               agev[m][i]=agedc[i];
+     fprintf(ficreseij,"\n");
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
+   }
-               if ((int)andc[i]!=9999){
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                 nbwarn++;
+   printf("\n");
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+   fprintf(ficlog,"\n");
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-                 agev[m][i]=-1;
+ }
-               }
-             }
+  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 )
-         }
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+ {
-                                  years but with the precision of a month */
+   /* Covariances of health expectancies eij and of total life expectancies according
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      to initial status i, ei. .
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+   */
-             agev[m][i]=1;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-           else if(agev[m][i] <agemin){
+   int nhstepma, nstepma; /* Decreasing with age */
-             agemin=agev[m][i];
+   double age, agelim, hf;
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+   double ***p3matp, ***p3matm, ***varhe;
-           }
+   double **dnewm,**doldm;
-           else if(agev[m][i] >agemax){
+   double *xp, *xm;
-             agemax=agev[m][i];
+   double **gp, **gm;
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   double ***gradg, ***trgradg;
-           }
+   int theta;
-           /*agev[m][i]=anint[m][i]-annais[i];*/
-           /*     agev[m][i] = age[i]+2*m;*/
+   double eip, vip;
-         }
-         else { /* =9 */
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-           agev[m][i]=1;
+   xp=vector(1,npar);
-           s[m][i]=-1;
+   xm=vector(1,npar);
-         }
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-       }
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-       else /*= 0 Unknown */
-         agev[m][i]=1;
+   pstamp(ficresstdeij);
-     }
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   fprintf(ficresstdeij,"# Age");
-   }
+   for(i=1; i<=nlstate;i++){
-   for (i=1; i<=imx; i++)  {
+     for(j=1; j<=nlstate;j++)
-     for(m=firstpass; (m<=lastpass); m++){
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       if (s[m][i] > (nlstate+ndeath)) {
+     fprintf(ficresstdeij," e%1d. ",i);
-         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(ficresstdeij,"\n");
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+   pstamp(ficrescveij);
-       }
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-     }
+   fprintf(ficrescveij,"# Age");
-   }
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
-   /*for (i=1; i<=imx; i++){
+       cptj= (j-1)*nlstate+i;
-   for (m=firstpass; (m<lastpass); m++){
+       for(i2=1; i2<=nlstate;i2++)
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+         for(j2=1; j2<=nlstate;j2++){
- }
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
- }*/
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         }
+     }
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   fprintf(ficrescveij,"\n");
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   if(estepm < stepm){
-   agegomp=(int)agemin;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   free_vector(severity,1,maxwav);
+   }
-   free_imatrix(outcome,1,maxwav+1,1,n);
+   else  hstepm=estepm;
-   free_vector(moisnais,1,n);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   free_vector(annais,1,n);
+    * This is mainly to measure the difference between two models: for example
-   /* free_matrix(mint,1,maxwav,1,n);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-      free_matrix(anint,1,maxwav,1,n);*/
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   free_vector(moisdc,1,n);
+    * progression in between and thus overestimating or underestimating according
-   free_vector(andc,1,n);
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
-   wav=ivector(1,imx);
+    * hypothesis. A more precise result, taking into account a more precise
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+    * curvature will be obtained if estepm is as small as stepm. */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* 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.
-   /* Concatenates waves */
+      nhstepm is the number of hstepm from age to agelim
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   Tcode=ivector(1,100);
+      survival function given by stepm (the optimization length). Unfortunately it
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+      means that if the survival funtion is printed only each two years of age and if
-   ncodemax[1]=1;
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+      results. So we changed our mind and took the option of the best precision.
+   */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-                                  the estimations*/
-   h=0;
+   /* If stepm=6 months */
-   m=pow(2,cptcoveff);
+   /* nhstepm age range expressed in number of stepm */
+   agelim=AGESUP;
-   for(k=1;k<=cptcoveff; k++){
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     for(i=1; i <=(m/pow(2,k));i++){
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(j=1; j <= ncodemax[k]; j++){
+   /* if (stepm >= YEARM) hstepm=1;*/
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       }
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     }
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   }
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-      codtab[1][2]=1;codtab[2][2]=2; */
+   for (age=bage; age<=fage; age ++){
-   /* for(i=1; i <=m ;i++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-      for(k=1; k <=cptcovn; k++){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+     /* if (stepm >= YEARM) hstepm=1;*/
-      }
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-      printf("\n");
-      }
+     /* If stepm=6 months */
-      scanf("%d",i);*/
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   /*------------ gnuplot -------------*/
-   strcpy(optionfilegnuplot,optionfilefiname);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+     /* Computing  Variances of health expectancies */
-   strcat(optionfilegnuplot,".gp");
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+        decrease memory allocation */
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     for(theta=1; theta <=npar; theta++){
-     printf("Problem with file %s",optionfilegnuplot);
+       for(i=1; i<=npar; i++){
-   }
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   else{
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-     fprintf(ficgp,"\n# %s\n", version);
+       }
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-     fprintf(ficgp,"set missing 'NaNq'\n");
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
-   }
-   /*  fclose(ficgp);*/
+       for(j=1; j<= nlstate; j++){
-   /*--------- index.htm --------*/
+         for(i=1; i<=nlstate; i++){
+           for(h=0; h<=nhstepm-1; h++){
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   if(mle==-3)
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-     strcat(optionfilehtm,"-mort");
+           }
-   strcat(optionfilehtm,".htm");
+         }
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+       }
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
+         for(h=0; h<=nhstepm-1; h++){
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   strcat(optionfilehtmcov,"-cov.htm");
+         }
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     }/* End theta */
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-   }
-   else{
+     for(h=0; h<=nhstepm-1; h++)
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+       for(j=1; j<=nlstate*nlstate;j++)
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         for(theta=1; theta <=npar; theta++)
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           trgradg[h][j][theta]=gradg[h][theta][j];
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-   }
+     for(ij=1;ij<=nlstate*nlstate;ij++)
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+       for(ji=1;ji<=nlstate*nlstate;ji++)
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         varhe[ij][ji][(int)age] =0.;
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
- \n\
+     printf("%d|",(int)age);fflush(stdout);
- <hr  size=\"2\" color=\"#EC5E5E\">\
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-  <ul><li><h4>Parameter files</h4>\n\
+     for(h=0;h<=nhstepm-1;h++){
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+       for(k=0;k<=nhstepm-1;k++){
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-  - Date and time at start: %s</ul>\n",\
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+       }
-           fileres,fileres,\
+     }
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-   fflush(fichtm);
+     /* Computing expectancies */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
-   strcpy(pathr,path);
+     for(i=1; i<=nlstate;i++)
-   strcat(pathr,optionfilefiname);
+       for(j=1; j<=nlstate;j++)
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+         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;
-   /* Calculates basic frequencies. Computes observed prevalence at single age
-      and prints on file fileres'p'. */
+           /* 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]);*/
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+         }
-   fprintf(fichtm,"\n");
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+     /* Standard deviation of expectancies ij */
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+     fprintf(ficresstdeij,"%3.0f",age );
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+     for(i=1; i<=nlstate;i++){
-           imx,agemin,agemax,jmin,jmax,jmean);
+       eip=0.;
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       vip=0.;
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       for(j=1; j<=nlstate;j++){
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         eip += eij[i][j][(int)age];
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-      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) */
+     fprintf(ficresstdeij,"\n");
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+     /* Variance of expectancies ij */
+     fprintf(ficrescveij,"%3.0f",age );
-   if (mle==-3){
+     for(i=1; i<=nlstate;i++)
-     ximort=matrix(1,NDIM,1,NDIM);
+       for(j=1; j<=nlstate;j++){
-     cens=ivector(1,n);
+         cptj= (j-1)*nlstate+i;
-     ageexmed=vector(1,n);
+         for(i2=1; i2<=nlstate;i2++)
-     agecens=vector(1,n);
+           for(j2=1; j2<=nlstate;j2++){
-     dcwave=ivector(1,n);
+             cptj2= (j2-1)*nlstate+i2;
+             if(cptj2 <= cptj)
-     for (i=1; i<=imx; i++){
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-       dcwave[i]=-1;
+           }
-       for (m=firstpass; m<=lastpass; m++)
+       }
-         if (s[m][i]>nlstate) {
+     fprintf(ficrescveij,"\n");
-           dcwave[i]=m;
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+   }
-           break;
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-         }
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     }
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     for (i=1; i<=imx; i++) {
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       if (wav[i]>0){
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         ageexmed[i]=agev[mw[1][i]][i];
+   printf("\n");
-         j=wav[i];
+   fprintf(ficlog,"\n");
-         agecens[i]=1.;
+   free_vector(xm,1,npar);
-         if (ageexmed[i]> 1 && wav[i] > 0){
+   free_vector(xp,1,npar);
-           agecens[i]=agev[mw[j][i]][i];
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-           cens[i]= 1;
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-         }else if (ageexmed[i]< 1)
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-           cens[i]= -1;
+ }
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           cens[i]=0 ;
+ /************ 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
-       else cens[i]=-1;
+  {
-     }
+    /** Variance of health expectancies
+     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
-     for (i=1;i<=NDIM;i++) {
+     * double **newm;
-       for (j=1;j<=NDIM;j++)
+     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     */
-     }
+    /* int movingaverage(); */
-     p[1]=0.0268; p[NDIM]=0.083;
+    double **dnewm,**doldm;
-     /*printf("%lf %lf", p[1], p[2]);*/
+    double **dnewmp,**doldmp;
+    int i, j, nhstepm, hstepm, h, nstepm ;
+    int first=0;
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+    int k;
-     strcpy(filerespow,"pow-mort");
+    double *xp;
-     strcat(filerespow,fileres);
+    double **gp, **gm;  /**< for var eij */
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+    double ***gradg, ***trgradg; /**< for var eij */
-       printf("Problem with resultfile: %s\n", filerespow);
+    double **gradgp, **trgradgp; /**< for var p point j */
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+    double *gpp, *gmp; /**< for var p point j */
-     }
+    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+    double ***p3mat;
-     /*  for (i=1;i<=nlstate;i++)
+    double age,agelim, hf;
-         for(j=1;j<=nlstate+ndeath;j++)
+    /* double ***mobaverage; */
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+    int theta;
-     */
+    char digit[4];
-     fprintf(ficrespow,"\n");
+    char digitp[25];
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+    char fileresprobmorprev[FILENAMELENGTH];
-     fclose(ficrespow);
+    if(popbased==1){
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+      if(mobilav!=0)
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-     for(i=1; i <=NDIM; i++)
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-       for(j=i+1;j<=NDIM;j++)
+    }
-         matcov[i][j]=matcov[j][i];
+    else
+      strcpy(digitp,"-STABLBASED_");
-     printf("\nCovariance matrix\n ");
-     for(i=1; i <=NDIM; i++) {
+    /* if (mobilav!=0) { */
-       for(j=1;j<=NDIM;j++){
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-         printf("%f ",matcov[i][j]);
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-       }
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-       printf("\n ");
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-     }
+    /*   } */
+    /* } */
-     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++)
+    strcpy(fileresprobmorprev,"PRMORPREV-");
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+    sprintf(digit,"%-d",ij);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-     lsurv=vector(1,AGESUP);
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
-     lpop=vector(1,AGESUP);
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-     tpop=vector(1,AGESUP);
+    strcat(fileresprobmorprev,fileresu);
-     lsurv[agegomp]=100000;
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
-     for (k=agegomp;k<=AGESUP;k++) {
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-       agemortsup=k;
+    }
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+    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);
-     for (k=agegomp;k<agemortsup;k++)
+    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);
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-     for (k=agegomp;k<agemortsup;k++){
+      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+    }
-       sumlpop=sumlpop+lpop[k];
+    for(j=1;j<=cptcoveff;j++)
-     }
+      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
+    fprintf(ficresprobmorprev,"\n");
-     tpop[agegomp]=sumlpop;
-     for (k=agegomp;k<(agemortsup-3);k++){
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-       /*  tpop[k+1]=2;*/
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       tpop[k+1]=tpop[k]-lpop[k];
+      fprintf(ficresprobmorprev," p.%-d SE",j);
-     }
+      for(i=1; i<=nlstate;i++)
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+    }
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+    fprintf(ficresprobmorprev,"\n");
-     for (k=agegomp;k<(agemortsup-2);k++)
-       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+    fprintf(ficgp,"\n# Routine varevsij");
+    fprintf(ficgp,"\nunset title \n");
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+    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");
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                      stepm, weightopt,\
+    pstamp(ficresvij);
-                      model,imx,p,matcov,agemortsup);
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+    if(popbased==1)
-     free_vector(lsurv,1,AGESUP);
+      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);
-     free_vector(lpop,1,AGESUP);
+    else
-     free_vector(tpop,1,AGESUP);
+      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   } /* Endof if mle==-3 */
+    fprintf(ficresvij,"# Age");
+    for(i=1; i<=nlstate;i++)
-   else{ /* For mle >=1 */
+      for(j=1; j<=nlstate;j++)
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+    fprintf(ficresvij,"\n");
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+    xp=vector(1,npar);
-       printf(" %d %8.5f",k,p[k]);
+    dnewm=matrix(1,nlstate,1,npar);
-     printf("\n");
+    doldm=matrix(1,nlstate,1,nlstate);
-     globpr=1; /* to print the contributions */
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-       printf(" %d %8.5f",k,p[k]);
+    gpp=vector(nlstate+1,nlstate+ndeath);
-     printf("\n");
+    gmp=vector(nlstate+1,nlstate+ndeath);
-     if(mle>=1){ /* Could be 1 or 2 */
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
+    if(estepm < stepm){
+      printf ("Problem %d lower than %d\n",estepm, stepm);
-     /*--------- 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);
+    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.
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       nhstepm is the number of hstepm from age to agelim
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       nstepm is the number of stepm from age to agelim.
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       Look at function hpijx to understand why because of memory size limitations,
-     for(i=1,jk=1; i <=nlstate; i++){
+       we decided (b) to get a life expectancy respecting the most precise curvature of the
-       for(k=1; k <=(nlstate+ndeath); k++){
+       survival function given by stepm (the optimization length). Unfortunately it
-         if (k != i) {
+       means that if the survival funtion is printed every two years of age and if
-           printf("%d%d ",i,k);
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
-           fprintf(ficlog,"%d%d ",i,k);
+       results. So we changed our mind and took the option of the best precision.
-           fprintf(ficres,"%1d%1d ",i,k);
+    */
-           for(j=1; j <=ncovmodel; j++){
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-             printf("%lf ",p[jk]);
+    agelim = AGESUP;
-             fprintf(ficlog,"%lf ",p[jk]);
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-             fprintf(ficres,"%lf ",p[jk]);
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-             jk++;
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           }
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           printf("\n");
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-           fprintf(ficlog,"\n");
+      gp=matrix(0,nhstepm,1,nlstate);
-           fprintf(ficres,"\n");
+      gm=matrix(0,nhstepm,1,nlstate);
-         }
-       }
-     }
+      for(theta=1; theta <=npar; theta++){
-     if(mle!=0){
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-       /* Computing hessian and covariance matrix */
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       ftolhess=ftol; /* Usually correct */
+        }
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
-     }
+         * returns into prlim .
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+         */
-     printf("# Scales (for hessian or gradient estimation)\n");
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-     for(i=1,jk=1; i <=nlstate; i++){
+        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
-       for(j=1; j <=nlstate+ndeath; j++){
+        if (popbased==1) {
-         if (j!=i) {
+          if(mobilav ==0){
-           fprintf(ficres,"%1d%1d",i,j);
+            for(i=1; i<=nlstate;i++)
-           printf("%1d%1d",i,j);
+              prlim[i][i]=probs[(int)age][i][ij];
-           fprintf(ficlog,"%1d%1d",i,j);
+          }else{ /* mobilav */
-           for(k=1; k<=ncovmodel;k++){
+            for(i=1; i<=nlstate;i++)
-             printf(" %.5e",delti[jk]);
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-             fprintf(ficlog," %.5e",delti[jk]);
+          }
-             fprintf(ficres," %.5e",delti[jk]);
+        }
-             jk++;
+        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
-           }
+         */
-           printf("\n");
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
-           fprintf(ficlog,"\n");
+        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
-           fprintf(ficres,"\n");
+         * 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++)
-     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");
+              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-     if(mle>=1)
+          }
-       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+        }
-     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");
+        /* Next for computing shifted+ probability of death (h=1 means
-     /* # 121 Var(a12)\n\ */
+           computed over hstepm matrices product = hstepm*stepm months)
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+        */
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+        }
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+        /* Again with minus shift */
-     /* Just to have a covariance matrix which will be more understandable
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-        even is we still don't want to manage dictionary of variables
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     */
-     for(itimes=1;itimes<=2;itimes++){
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
-       jj=0;
-       for(i=1; i <=nlstate; i++){
+        if (popbased==1) {
-         for(j=1; j <=nlstate+ndeath; j++){
+          if(mobilav ==0){
-           if(j==i) continue;
+            for(i=1; i<=nlstate;i++)
-           for(k=1; k<=ncovmodel;k++){
+              prlim[i][i]=probs[(int)age][i][ij];
-             jj++;
+          }else{ /* mobilav */
-             ca[0]= k+'a'-1;ca[1]='\0';
+            for(i=1; i<=nlstate;i++)
-             if(itimes==1){
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-               if(mle>=1)
+          }
-                 printf("#%1d%1d%d",i,j,k);
+        }
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
-             }else{
-               if(mle>=1)
+        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-                 printf("%1d%1d%d",i,j,k);
+          for(h=0; h<=nhstepm; h++){
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-             }
+          }
-             ll=0;
+        }
-             for(li=1;li <=nlstate; li++){
+        /* This for computing probability of death (h=1 means
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+           computed over hstepm matrices product = hstepm*stepm months)
-                 if(lj==li) continue;
+           as a weighted average of prlim.
-                 for(lk=1;lk<=ncovmodel;lk++){
+        */
-                   ll++;
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                   if(ll<=jj){
+          for(i=1,gmp[j]=0.; i<= nlstate; i++)
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+            gmp[j] += prlim[i][i]*p3mat[i][j][1];
-                     if(ll<jj){
+        }
-                       if(itimes==1){
+        /* end shifting computations */
-                         if(mle>=1)
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+        /**< Computing gradient matrix at horizon h
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         */
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+        for(j=1; j<= nlstate; j++) /* vareij */
-                       }else{
+          for(h=0; h<=nhstepm; h++){
-                         if(mle>=1)
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-                           printf(" %.5e",matcov[jj][ll]);
+          }
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+        /**< Gradient of overall mortality p.3 (or p.j)
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+         */
-                       }
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
-                     }else{
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-                       if(itimes==1){
+        }
-                         if(mle>=1)
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+      } /* End theta */
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+      /* We got the gradient matrix for each theta and state j */
-                       }else{
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+      for(h=0; h<=nhstepm; h++) /* veij */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+        for(j=1; j<=nlstate;j++)
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+          for(theta=1; theta <=npar; theta++)
-                       }
+            trgradg[h][j][theta]=gradg[h][theta][j];
-                     }
-                   }
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-                 } /* end lk */
+        for(theta=1; theta <=npar; theta++)
-               } /* end lj */
+          trgradgp[j][theta]=gradgp[theta][j];
-             } /* end li */
+      /**< as well as its transposed matrix
-             if(mle>=1)
+       */
-               printf("\n");
-             fprintf(ficlog,"\n");
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-             fprintf(ficres,"\n");
+      for(i=1;i<=nlstate;i++)
-             numlinepar++;
+        for(j=1;j<=nlstate;j++)
-           } /* end k*/
+          vareij[i][j][(int)age] =0.;
-         } /*end j */
-       } /* end i */
+      /* Computing trgradg by matcov by gradg at age and summing over h
-     } /* end itimes */
+       * and k (nhstepm) formula 15 of article
+       * Lievre-Brouard-Heathcote
-     fflush(ficlog);
+       */
-     fflush(ficres);
+      for(h=0;h<=nhstepm;h++){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+        for(k=0;k<=nhstepm;k++){
-       ungetc(c,ficpar);
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-       fgets(line, MAXLINE, ficpar);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-       puts(line);
+          for(i=1;i<=nlstate;i++)
-       fputs(line,ficparo);
+            for(j=1;j<=nlstate;j++)
-     }
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-     ungetc(c,ficpar);
+        }
+      }
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+       * p.j overall mortality formula 49 but computed directly because
-     if (fage <= 2) {
+       * we compute the grad (wix pijx) instead of grad (pijx),even if
-       bage = ageminpar;
+       * wix is independent of theta.
-       fage = agemaxpar;
+       */
-     }
+      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);
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+          varppt[j][i]=doldmp[j][i];
+      /* end ppptj */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      /*  x centered again */
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
-       puts(line);
-       fputs(line,ficparo);
+      if (popbased==1) {
-     }
+        if(mobilav ==0){
-     ungetc(c,ficpar);
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
-     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);
+        }else{ /* 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);
+          for(i=1; i<=nlstate;i++)
-     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);
+            prlim[i][i]=mobaverage[(int)age][i][ij];
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+        }
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+      }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      /* This for computing probability of death (h=1 means
-       ungetc(c,ficpar);
+         computed over hstepm (estepm) matrices product = hstepm*stepm months)
-       fgets(line, MAXLINE, ficpar);
+         as a weighted average of prlim.
-       puts(line);
+      */
-       fputs(line,ficparo);
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
-     }
+      for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     ungetc(c,ficpar);
+        for(i=1,gmp[j]=0.;i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+      }
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+      /* end probability of death */
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-     fprintf(ficres,"pop_based=%d\n",popbased);
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+        }
-       ungetc(c,ficpar);
+      }
-       fgets(line, MAXLINE, ficpar);
+      fprintf(ficresprobmorprev,"\n");
-       puts(line);
-       fputs(line,ficparo);
+      fprintf(ficresvij,"%.0f ",age );
-     }
+      for(i=1; i<=nlstate;i++)
-     ungetc(c,ficpar);
+        for(j=1; j<=nlstate;j++){
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+        }
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+      fprintf(ficresvij,"\n");
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+      free_matrix(gp,0,nhstepm,1,nlstate);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+      free_matrix(gm,0,nhstepm,1,nlstate);
-     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);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-     /* day and month of proj2 are not used but only year anproj2.*/
+      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);
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+    free_vector(gmp,nlstate+1,nlstate+ndeath);
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*   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); */
-    /*------------ free_vector  -------------*/
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-    /*  chdir(path); */
+    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));
-     free_ivector(wav,1,imx);
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+    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);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+    /*  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);
-     free_lvector(num,1,n);
+     */
-     free_vector(agedc,1,n);
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
+    free_vector(xp,1,npar);
-     fclose(ficres);
+    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);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     strcpy(filerespl,"pl");
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-     strcat(filerespl,fileres);
+    fclose(ficresprobmorprev);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+    fflush(ficgp);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+    fflush(fichtm);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+  }  /* end varevsij */
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ /************ Variance of prevlim ******************/
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+  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)
-     pstamp(ficrespl);
+ {
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-     fprintf(ficrespl,"#Age ");
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-     fprintf(ficrespl,"\n");
+   double **dnewmpar,**doldm;
+   int i, j, nhstepm, hstepm;
-     prlim=matrix(1,nlstate,1,nlstate);
+   double *xp;
+   double *gp, *gm;
-     agebase=ageminpar;
+   double **gradg, **trgradg;
-     agelim=agemaxpar;
+   double **mgm, **mgp;
-     ftolpl=1.e-10;
+   double age,agelim;
-     i1=cptcoveff;
+   int theta;
-     if (cptcovn < 1){i1=1;}
+   pstamp(ficresvpl);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   fprintf(ficresvpl,"# Age ");
-         k=k+1;
+   if(nresult >=1)
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     fprintf(ficresvpl," Result# ");
-         fprintf(ficrespl,"\n#******");
+   for(i=1; i<=nlstate;i++)
-         printf("\n#******");
+       fprintf(ficresvpl," %1d-%1d",i,i);
-         fprintf(ficlog,"\n#******");
+   fprintf(ficresvpl,"\n");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   xp=vector(1,npar);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   dnewmpar=matrix(1,nlstate,1,npar);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   doldm=matrix(1,nlstate,1,nlstate);
-         }
-         fprintf(ficrespl,"******\n");
+   hstepm=1*YEARM; /* Every year of age */
-         printf("******\n");
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-         fprintf(ficlog,"******\n");
+   agelim = AGESUP;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         for (age=agebase; age<=agelim; age++){
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     if (stepm >= YEARM) hstepm=1;
-           fprintf(ficrespl,"%.0f ",age );
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           for(j=1;j<=cptcoveff;j++)
+     gradg=matrix(1,npar,1,nlstate);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     mgp=matrix(1,npar,1,nlstate);
-           for(i=1; i<=nlstate;i++)
+     mgm=matrix(1,npar,1,nlstate);
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+     gp=vector(1,nlstate);
-           fprintf(ficrespl,"\n");
+     gm=vector(1,nlstate);
-         }
-       }
+     for(theta=1; theta <=npar; theta++){
-     }
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-     fclose(ficrespl);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
-     /*------------- h Pij x at various ages ------------*/
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+       /* else */
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       for(i=1;i<=nlstate;i++){
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+         gp[i] = prlim[i][i];
-     }
+         mgp[theta][i] = prlim[i][i];
-     printf("Computing pij: result on file '%s' \n", filerespij);
+       }
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+       for(i=1; i<=npar; i++) /* Computes gradient */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-     /*if (stepm<=24) stepsize=2;*/
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
+       /* else */
-     agelim=AGESUP;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
-     hstepm=stepsize*YEARM; /* Every year of age */
+       for(i=1;i<=nlstate;i++){
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+         gm[i] = prlim[i][i];
+         mgm[theta][i] = prlim[i][i];
-     /* hstepm=1;   aff par mois*/
+       }
-     pstamp(ficrespij);
+       for(i=1;i<=nlstate;i++)
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     } /* End theta */
-         k=k+1;
-         fprintf(ficrespij,"\n#****** ");
+     trgradg =matrix(1,nlstate,1,npar);
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(j=1; j<=nlstate;j++)
-         fprintf(ficrespij,"******\n");
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     /*   printf("\nmgm mgp %d ",(int)age); */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /*  printf("\n "); */
-           oldm=oldms;savm=savms;
+     /*   } */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     /* } */
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-           for(i=1; i<=nlstate;i++)
+     /*   printf("\n gradg %d ",(int)age); */
-             for(j=1; j<=nlstate+ndeath;j++)
+     /*   for(j=1; j<=nlstate;j++){ */
-               fprintf(ficrespij," %1d-%1d",i,j);
+     /*  printf("%d ",j); */
-           fprintf(ficrespij,"\n");
+     /*  for(theta=1; theta <=npar; theta++) */
-           for (h=0; h<=nhstepm; h++){
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+     /*  printf("\n "); */
-             for(i=1; i<=nlstate;i++)
+     /*   } */
-               for(j=1; j<=nlstate+ndeath;j++)
+     /* } */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
+     for(i=1;i<=nlstate;i++)
-           }
+       varpl[i][(int)age] =0.;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-           fprintf(ficrespij,"\n");
+     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);
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     }
+     for(i=1;i<=nlstate;i++)
-     fclose(ficrespij);
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1;i<=AGESUP;i++)
+     if(nresult >=1)
-       for(j=1;j<=NCOVMAX;j++)
+       fprintf(ficresvpl,"%d ",nres );
-         for(k=1;k<=NCOVMAX;k++)
+     for(i=1; i<=nlstate;i++){
-           probs[i][j][k]=0.;
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       /* for(j=1;j<=nlstate;j++) */
-     /*---------- Forecasting ------------------*/
+       /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     }
-     if(prevfcast==1){
+     fprintf(ficresvpl,"\n");
-       /*    if(stepm ==1){*/
+     free_vector(gp,1,nlstate);
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+     free_vector(gm,1,nlstate);
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     free_matrix(mgm,1,npar,1,nlstate);
-       /*      }  */
+     free_matrix(mgp,1,npar,1,nlstate);
-       /*      else{ */
+     free_matrix(gradg,1,npar,1,nlstate);
-       /*        erreur=108; */
+     free_matrix(trgradg,1,nlstate,1,npar);
-       /*        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); */
+   } /* End age */
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*      } */
+   free_vector(xp,1,npar);
-     }
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
-     /*---------- Health expectancies and variances ------------*/
+ }
-     strcpy(filerest,"t");
-     strcat(filerest,fileres);
+ /************ Variance of backprevalence limit ******************/
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+  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)
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+ {
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   /* 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);*/
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   double **dnewmpar,**doldm;
+   int i, j, nhstepm, hstepm;
+   double *xp;
-     strcpy(filerese,"e");
+   double *gp, *gm;
-     strcat(filerese,fileres);
+   double **gradg, **trgradg;
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   double **mgm, **mgp;
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   double age,agelim;
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   int theta;
-     }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   pstamp(ficresvbl);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
+   fprintf(ficresvbl,"# Age ");
-     strcpy(fileresstde,"stde");
+   if(nresult >=1)
-     strcat(fileresstde,fileres);
+     fprintf(ficresvbl," Result# ");
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   for(i=1; i<=nlstate;i++)
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficresvbl," %1d-%1d",i,i);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   fprintf(ficresvbl,"\n");
-     }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   xp=vector(1,npar);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   dnewmpar=matrix(1,nlstate,1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
-     strcpy(filerescve,"cve");
-     strcat(filerescve,fileres);
+   hstepm=1*YEARM; /* Every year of age */
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   agelim = AGEINF;
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   for (age=fage; age>=bage; age --){ /* If stepm=6 months */
-     }
+     nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     if (stepm >= YEARM) hstepm=1;
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     gradg=matrix(1,npar,1,nlstate);
-     strcpy(fileresv,"v");
+     mgp=matrix(1,npar,1,nlstate);
-     strcat(fileresv,fileres);
+     mgm=matrix(1,npar,1,nlstate);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     gp=vector(1,nlstate);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     gm=vector(1,nlstate);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-     }
+     for(theta=1; theta <=npar; theta++){
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+       if(mobilavproj > 0 )
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-     /*  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",\
+       else
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-     */
+       for(i=1;i<=nlstate;i++){
+         gp[i] = bprlim[i][i];
-     if (mobilav!=0) {
+         mgp[theta][i] = bprlim[i][i];
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       }
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+      for(i=1; i<=npar; i++) /* Computes gradient */
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+        if(mobilavproj > 0 )
-       }
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-     }
+        else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(i=1;i<=nlstate;i++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         gm[i] = bprlim[i][i];
-         k=k+1;
+         mgm[theta][i] = bprlim[i][i];
-         fprintf(ficrest,"\n#****** ");
+       }
-         for(j=1;j<=cptcoveff;j++)
+       for(i=1;i<=nlstate;i++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-         fprintf(ficrest,"******\n");
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
+     } /* End theta */
-         fprintf(ficreseij,"\n#****** ");
-         fprintf(ficresstdeij,"\n#****** ");
+     trgradg =matrix(1,nlstate,1,npar);
-         fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+     for(j=1; j<=nlstate;j++)
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for(theta=1; theta <=npar; theta++)
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         trgradg[j][theta]=gradg[theta][j];
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-         }
+     /*   printf("\nmgm mgp %d ",(int)age); */
-         fprintf(ficreseij,"******\n");
+     /*   for(j=1; j<=nlstate;j++){ */
-         fprintf(ficresstdeij,"******\n");
+     /*  printf(" %d ",j); */
-         fprintf(ficrescveij,"******\n");
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
-         fprintf(ficresvij,"\n#****** ");
+     /*  printf("\n "); */
-         for(j=1;j<=cptcoveff;j++)
+     /*   } */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     /* } */
-         fprintf(ficresvij,"******\n");
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     /*   for(j=1; j<=nlstate;j++){ */
-         oldm=oldms;savm=savms;
+     /*  printf("%d ",j); */
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+     /*  for(theta=1; theta <=npar; theta++) */
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     /*   } */
-         oldm=oldms;savm=savms;
+     /* } */
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
-         if(popbased==1){
+     for(i=1;i<=nlstate;i++)
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+       varbpl[i][(int)age] =0.;
-         }
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-         pstamp(ficrest);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     }else{
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-         fprintf(ficrest,"\n");
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }
-         epj=vector(1,nlstate+1);
+     for(i=1;i<=nlstate;i++)
-         for(age=bage; age <=fage ;age++){
+       varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           if (popbased==1) {
+     fprintf(ficresvbl,"%.0f ",age );
-             if(mobilav ==0){
+     if(nresult >=1)
-               for(i=1; i<=nlstate;i++)
+       fprintf(ficresvbl,"%d ",nres );
-                 prlim[i][i]=probs[(int)age][i][k];
+     for(i=1; i<=nlstate;i++)
-             }else{ /* mobilav */
+       fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
-               for(i=1; i<=nlstate;i++)
+     fprintf(ficresvbl,"\n");
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     free_vector(gp,1,nlstate);
-             }
+     free_vector(gm,1,nlstate);
-           }
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
-           fprintf(ficrest," %4.0f",age);
+     free_matrix(gradg,1,npar,1,nlstate);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     free_matrix(trgradg,1,nlstate,1,npar);
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   } /* End age */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+   free_vector(xp,1,npar);
-             }
+   free_matrix(doldm,1,nlstate,1,npar);
-             epj[nlstate+1] +=epj[j];
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
-           }
+ }
-           for(i=1, vepp=0.;i <=nlstate;i++)
-             for(j=1;j <=nlstate;j++)
+ /************ Variance of one-step probabilities  ******************/
-               vepp += vareij[i][j][(int)age];
+ 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[])
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+  {
-           for(j=1;j <=nlstate;j++){
+    int i, j=0,  k1, l1, tj;
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+    int k2, l2, j1,  z1;
-           }
+    int k=0, l;
-           fprintf(ficrest,"\n");
+    int first=1, first1, first2;
-         }
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+    double **dnewm,**doldm;
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+    double *xp;
-         free_vector(epj,1,nlstate+1);
+    double *gp, *gm;
-       }
+    double **gradg, **trgradg;
-     }
+    double **mu;
-     free_vector(weight,1,n);
+    double age, cov[NCOVMAX+1];
-     free_imatrix(Tvard,1,15,1,2);
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-     free_imatrix(s,1,maxwav+1,1,n);
+    int theta;
-     free_matrix(anint,1,maxwav,1,n);
+    char fileresprob[FILENAMELENGTH];
-     free_matrix(mint,1,maxwav,1,n);
+    char fileresprobcov[FILENAMELENGTH];
-     free_ivector(cod,1,n);
+    char fileresprobcor[FILENAMELENGTH];
-     free_ivector(tab,1,NCOVMAX);
+    double ***varpij;
-     fclose(ficreseij);
-     fclose(ficresstdeij);
+    strcpy(fileresprob,"PROB_");
-     fclose(ficrescveij);
+    strcat(fileresprob,fileres);
-     fclose(ficresvij);
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-     fclose(ficrest);
+      printf("Problem with resultfile: %s\n", fileresprob);
-     fclose(ficpar);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+    }
-     /*------- Variance of period (stable) prevalence------*/
+    strcpy(fileresprobcov,"PROBCOV_");
+    strcat(fileresprobcov,fileresu);
-     strcpy(fileresvpl,"vpl");
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     strcat(fileresvpl,fileres);
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+    }
-       exit(0);
+    strcpy(fileresprobcor,"PROBCOR_");
-     }
+    strcat(fileresprobcor,fileresu);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+    }
-         k=k+1;
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-         fprintf(ficresvpl,"\n#****** ");
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-         for(j=1;j<=cptcoveff;j++)
+    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-         fprintf(ficresvpl,"******\n");
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+    pstamp(ficresprob);
-         oldm=oldms;savm=savms;
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+    fprintf(ficresprob,"# Age");
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+    pstamp(ficresprobcov);
-       }
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-     }
+    fprintf(ficresprobcov,"# Age");
+    pstamp(ficresprobcor);
-     fclose(ficresvpl);
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    fprintf(ficresprobcor,"# Age");
-     /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    for(i=1; i<=nlstate;i++)
+      for(j=1; j<=(nlstate+ndeath);j++){
-   }  /* mle==-3 arrives here for freeing */
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-   free_matrix(prlim,1,nlstate,1,nlstate);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+      }
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+    /* fprintf(ficresprob,"\n");
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       fprintf(ficresprobcov,"\n");
-     free_matrix(covar,0,NCOVMAX,1,n);
+       fprintf(ficresprobcor,"\n");
-     free_matrix(matcov,1,npar,1,npar);
+    */
-     /*free_vector(delti,1,npar);*/
+    xp=vector(1,npar);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-     free_matrix(agev,1,maxwav,1,imx);
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-     free_ivector(ncodemax,1,8);
+    first=1;
-     free_ivector(Tvar,1,15);
+    fprintf(ficgp,"\n# Routine varprob");
-     free_ivector(Tprod,1,15);
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-     free_ivector(Tvaraff,1,15);
+    fprintf(fichtm,"\n");
-     free_ivector(Tage,1,15);
-     free_ivector(Tcode,1,100);
+    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);
+    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);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-     free_imatrix(codtab,1,100,1,10);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   fflush(fichtm);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   fflush(ficgp);
+    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 \
-   if((nberr >0) || (nbwarn>0)){
+ standard deviations wide on each axis. <br>\
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-   }else{
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-     printf("End of Imach\n");
-     fprintf(ficlog,"End of Imach\n");
+    cov[1]=1;
-   }
+    /* tj=cptcoveff; */
-   printf("See log file on %s\n",filelog);
+    tj = (int) pow(2,cptcoveff);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   (void) gettimeofday(&end_time,&tzp);
+    j1=0;
-   tm = *localtime(&end_time.tv_sec);
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
-   tmg = *gmtime(&end_time.tv_sec);
+      if  (cptcovn>0) {
-   strcpy(strtend,asctime(&tm));
+        fprintf(ficresprob, "\n#********** Variable ");
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+        fprintf(ficresprob, "**********\n#\n");
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+        fprintf(ficresprobcov, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+        fprintf(ficresprobcov, "**********\n#\n");
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+        fprintf(ficgp, "\n#********** Variable ");
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+        fprintf(ficgp, "**********\n#\n");
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
-   fclose(fichtm);
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-   fclose(fichtmcov);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   fclose(ficgp);
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-   fclose(ficlog);
-   /*------ End -----------*/
+        fprintf(ficresprobcor, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        fprintf(ficresprobcor, "**********\n#");
-    printf("Before Current directory %s!\n",pathcd);
+        if(invalidvarcomb[j1]){
-    if(chdir(pathcd) != 0)
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-     printf("Can't move to directory %s!\n",path);
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
-   if(getcwd(pathcd,MAXLINE) > 0)
+          continue;
-     printf("Current directory %s!\n",pathcd);
+        }
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+      }
-   sprintf(plotcmd,"gnuplot");
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
- #ifndef UNIX
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
- #endif
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-   if(!stat(plotcmd,&info)){
+      for (age=bage; age<=fage; age ++){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+        cov[2]=age;
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+        if(nagesqr==1)
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+          cov[3]= age*age;
-     }else
+        for (k=1; k<=cptcovn;k++) {
-       strcpy(pplotcmd,plotcmd);
+          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
- #ifdef UNIX
+          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+                                                                     * 1  1 1 1 1
-     if(!stat(plotcmd,&info)){
+                                                                     * 2  2 1 1 1
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+                                                                     * 3  1 2 1 1
-     }else
+                                                                     */
-       strcpy(pplotcmd,plotcmd);
+          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
- #endif
+        }
-   }else
+        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     strcpy(pplotcmd,plotcmd);
+        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+        for (k=1; k<=cptcovprod;k++)
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
-   if((outcmd=system(plotcmd)) != 0){
+        for(theta=1; theta <=npar; theta++){
-     printf("\n Problem with gnuplot\n");
+          for(i=1; i<=npar; i++)
-   }
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-   printf(" Wait...");
-   while (z[0] != 'q') {
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+          k=0;
-     scanf("%s",z);
+          for(i=1; i<= (nlstate); i++){
- /*     if (z[0] == 'c') system("./imach"); */
+            for(j=1; j<=(nlstate+ndeath);j++){
-     if (z[0] == 'e') {
+              k=k+1;
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+              gp[k]=pmmij[i][j];
-       system(optionfilehtm);
+            }
-     }
+          }
-     else if (z[0] == 'g') system(plotcmd);
-     else if (z[0] == 'q') exit(0);
+          for(i=1; i<=npar; i++)
-   }
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-   end:
-   while (z[0] != 'q') {
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     printf("\nType  q for exiting: ");
+          k=0;
-     scanf("%s",z);
+          for(i=1; i<=(nlstate); i++){
-   }
+            for(j=1; j<=(nlstate+ndeath);j++){
- }
+              k=k+1;
+              gm[k]=pmmij[i][j];
+            }
+          }
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+        }
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+          for(theta=1; theta <=npar; theta++)
+            trgradg[j][theta]=gradg[theta][j];
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
+        k=0;
+        for(i=1; i<=(nlstate); i++){
+          for(j=1; j<=(nlstate+ndeath);j++){
+            k=k+1;
+            mu[k][(int) age]=pmmij[i][j];
+          }
+        }
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+            varpij[i][j][(int)age] = doldm[i][j];
+        /*printf("\n%d ",(int)age);
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          }*/
+        fprintf(ficresprob,"\n%d ",(int)age);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+        }
+        i=0;
+        for (k=1; k<=(nlstate);k++){
+          for (l=1; l<=(nlstate+ndeath);l++){
+            i++;
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+            for (j=1; j<=i;j++){
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+            }
+          }
+        }/* end of loop for state */
+      } /* end of loop for age */
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      /* Confidence intervalle of pij  */
+      /*
+        fprintf(ficgp,"\nunset parametric;unset label");
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+        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 */
+    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 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 mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
+                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
+   int jj1, k1, i1, cpt, k4, nres;
+    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> model=1+age+%s\n \
+ </ul>", model);
+    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 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(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
+    fprintf(fichtm,"\
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
+    fprintf(fichtm,"\
+  - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
+    fprintf(fichtm,"\
+  - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            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_"));
+    }
+    m=pow(2,cptcoveff);
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    jj1=0;
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    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<=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<=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 */
+    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<=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,"\"</a>");
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* 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); */
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+       }
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        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>\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-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
+      /* Quasi-incidences */
+      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, \
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
+ 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> \
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,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> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,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> \
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+      }
+      if(backcast==1){
+        /* Backward prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          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-%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><br> \
+ <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+        }
+      }
+      if(backcast==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><br> \
+  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,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) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
+ <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+      }
+      /* } /\* end i1 *\/ */
+    }/* End k1 */
+    fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"\
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+  - 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," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
+    fprintf(fichtm,"\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
+    fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
+    fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
+    fprintf(fichtm,"\
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
+    fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the 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(fileresu,"V_"),subdirf2(fileresu,"V_"));
+    fprintf(fichtm,"\
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
+    fprintf(fichtm,"\
+  - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+ /*      <br>",fileres,fileres,fileres,fileres); */
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+    fflush(fichtm);
+    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    m=pow(2,cptcoveff);
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+    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,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,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," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
+        }
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
+ <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,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) \
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
+ <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
+      /* } /\* end i1 *\/ */
+    }/* End k1 */
+   }/* End nres */
+    fprintf(fichtm,"</ul>");
+    fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
+   char dirfileres[132],optfileres[132];
+   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); */
+ /*   } */
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   /*#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*/
+   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
+     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+         if(m != 1 && TKresult[nres]!= k1)
+           continue;
+         /* We are interested in selected combination by the resultline */
+         /* 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);
+         strcpy(gplotlabel,"(");
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate 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 is the value of the covariate lv, 0 or 1 */
+           /* 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," 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 */
+           /* 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),")");
+         /* printf("\n#\n"); */
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           /*k1=k1-1;*/ /* To be checked */
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,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 title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
+         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); */
+       /* 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\"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);
+         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 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%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 */
+             /* 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 && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+               kl++;
+             }
+           } /* end covariate */
+         } /* end if no covariate */
+         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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 */
+               /* 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)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               }else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+           if(backcast == 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 backcast */
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
+       } /* nres */
+     } /* k1 */
+   } /* cpt */
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       strcpy(gplotlabel,"(");
+       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 */
+         /* 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];
+         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*/
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         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 */
+           /* 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];
+           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][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;
+         }
+         /*       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 */
+       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 j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+         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 */
+           /* 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];
+           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][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-%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 */
+       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<=cptcoveff; k++){    /* For each covariate and each value */
+           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];
+           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][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-%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 */
+     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<=cptcoveff; k++){    /* For each covariate and each value */
+         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];
+         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][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-%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 svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3; /* Offset */
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
+         if(i==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out; unset label;\n");
+     } /* end cpt state*/
+   } /* end covariate */
+ /* 7eme */
+   if(backcast == 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 */
+       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<=cptcoveff; k++){    /* For each covariate and each value */
+           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];
+           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][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-%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 backcast */
+   /* 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 */
+       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<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* 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];
+           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][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,"# 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 */
+               /* 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] */
+               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(backcast==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 */
+       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<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* 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];
+           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][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,"# 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<=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 */
+               /* 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] */
+               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 : 1/0):%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 backcast */
+   /* 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]);
+           jk++;
+         }
+         fprintf(ficgp,"\n");
+       }
+     }
+   }
+   fprintf(ficgp,"##############\n#\n");
+   /*goto avoid;*/
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
+   fprintf(ficgp,"#\n");
+   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
+     fprintf(ficgp,"#model=%s \n",model);
+     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
+     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
+       strcpy(gplotlabel,"(");
+       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
+       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 */
+         /* 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];
+         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][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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); */
+               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!!*/
+                   if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                     if(DummyV[j]==0){
+                       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++;
+                   }
+                 }
+               }else 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 */
+               } else{  /* 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 */
+             } /* end j */
+           }else{
+             i=i-ncovmodel;
+             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");
+           }
+           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;
+               for(j=3; j <=ncovmodel-nagesqr; j++){
+                  if(cptcovage >0){
+                    if((j-2)==Tage[ij]) { /* Bug valgrind */
+                      if(ij <=cptcovage) { /* 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-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                        ij++;
+                      }
+                    }
+                  }else
+                    fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
+               }
+               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 k1 */
+   } /* end ng */
+   /* avoid: */
+   fflush(ficgp);
+ }  /* end gnuplot */
+ /*************** Moving average **************/
+ /* 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;
+    }
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
+      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
+      if(invalidvarcomb[cptcod]){
+        printf("\nCombination (%d) ignored because no cases \n",cptcod);
+        continue;
+      }
+      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
+        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(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemingoodr[cptcod]=age;
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingood[cptcod]=age;
+        }
+      } /* age */
+      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
+        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(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemaxgoodr[cptcod]=age;
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemaxgood[cptcod]=age;
+        }
+      } /* age */
+      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
+      /* 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 ******************/
+  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+   /* proj1, year, month, day of starting projection
+      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, k4, nres=0;
+   double agec; /* generic age */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   /* double ***mobaverage; */
+   char fileresf[FILENAMELENGTH];
+   agelim=AGESUP;
+   /* 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_");
+   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("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
+   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 */
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=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(ficresf,"#****** Routine prevforecast **\n");
+ /*            if (h==(int)(YEARM*yearp)){ */
+   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(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,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<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+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,j)]);
+         fprintf(ficresf,"%.f %.f ",anproj1+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){
+   /* back1, year, month, day of starting backection
+      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,jprojmean,mprojmean,anprojmean;
+   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?*/
+   /* 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 */
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
+   i1=pow(2,cptcoveff);
+   if (cptcovn < 1){i1=1;}
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   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,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>=(anback2-anback1);yearp -=stepsize) {
+       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
+       fprintf(ficresfb,"\n");
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+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,j)]);
+         fprintf(ficresfb,"%.f %.f ",anback1+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");
+ }
+ /* Variance of prevalence limit: varprlim */
+  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){
+     /*------- Variance of forward period (stable) prevalence------*/
+    char fileresvpl[FILENAMELENGTH];
+    FILE *ficresvpl;
+    double **oldm, **savm;
+    double **varpl; /* Variances of prevalence limits by age */
+    int i1, k, nres, j ;
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     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(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+       fprintf(ficresvpl,"\n#****** ");
+       printf("\n#****** ");
+       fprintf(ficlog,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
+  }
+ /* 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 */
+      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<=cptcoveff;j++) {
+          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+        }
+        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+        }
+        fprintf(ficresvbl,"******\n");
+        printf("******\n");
+        fprintf(ficlog,"******\n");
+        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);
+  } /* End of varbprlim */
+ /************** Forecasting *****not tested NB*************/
+ /* 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); */
+ /*   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 (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; */
+ /*   agelim=AGESUP; */
+ /*   hstepm=1; */
+ /*   hstepm=hstepm/stepm;  */
+ /*   if (popforecast==1) { */
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
+ /*     }  */
+ /*     popage=ivector(0,AGESUP); */
+ /*     popeffectif=vector(0,AGESUP); */
+ /*     popcount=vector(0,AGESUP); */
+ /*     i=1;    */
+ /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
+ /*     imx=i; */
+ /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
+ /*   } */
+ /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
+ /*       k=k+1; */
+ /*       fprintf(ficrespop,"\n#******"); */
+ /*       for(j=1;j<=cptcoveff;j++) { */
+ /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+ /*       } */
+ /*       fprintf(ficrespop,"******\n"); */
+ /*       fprintf(ficrespop,"# Age"); */
+ /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
+ /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
+ /*       for (cpt=0; cpt<=0;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(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); */
+ /*        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 *\/ */
+ int fileappend(FILE *fichier, char *optionfich)
+ {
+   if((fichier=fopen(optionfich,"a"))==NULL) {
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
+   }
+   fflush(fichier);
+   return (1);
+ }
+ /**************** function prwizard **********************/
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
+   /* Wizard to print covariance matrix template */
+   char ca[32], cb[32];
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
+       printf("%1d%1d",i,j);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
+       numlinepar++;
+       printf("\n");
+       fprintf(ficparo,"\n");
+     }
+   }
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
+             printf("%1d%1d%d",i,j,k);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }else{
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
+                   }
+                 }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
+           printf("\n");
+           fprintf(ficparo,"\n");
+           numlinepar++;
+         } /* end k*/
+       } /*end j */
+     } /* end i */
+   } /* end itimes */
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=1;i<=imx ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   return -2*L*num/sump;
+ }
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
+ double gompertz_f(const gsl_vector *v, void *params)
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
+   }
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+   for (i=1;i<=imx ; i++)
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+   return -2*LL*num/sump;
+ }
+ #endif
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char 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;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
+   fprintf(fichtm,"</ul>");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
+   int ng;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   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 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);
+ }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+ {
+   /*-------- data file ----------*/
+   FILE *fic;
+   char dummy[]="                         ";
+   int i=0, j=0, n=0, iv=0, v;
+   int lstra;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[MAXLINE], strb[MAXLINE];
+   char *stratrunc;
+   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   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 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;
+   }
+   i=1;
+   linei=0;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       if(line[j] == '\t')
+         line[j] = ' ';
+     }
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
+       continue;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     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 (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
+         V1=1 V2=0 for (2) \n                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                \
+  Exiting.\n",lval,linei, i,line,j);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
+         V1=1 V2=0 for (2) \n                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+           return 1;
+         }
+         cotvar[j][iv][i]=(double)(lval);
+         strcpy(line,stra);
+       }/* end loop ntv */
+       /* Statuses  at wave */
+       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 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){
+       }
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
+         month=99;
+         year=9999;
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         return 1;
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* End loop on waves */
+     /* Date of death */
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+       return 1;
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     /* Date of birth */
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+       return 1;
+     }
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+       return 1;
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     /* Sample weight */
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fflush(ficlog);
+       return 1;
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing value */
+         lval=-1;
+       }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 covariate value */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           return 1;
+         }
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
+         V1=1 V2=0 for (2) \n                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                \
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
+         V1=1 V2=0 for (2) \n                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+         return 1;
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
+   return (0);
+   /* endread: */
+   printf("Exiting readdata: ");
+   fclose(fic);
+   return (1);
+ }
+ void 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);
+   if (strstr(resultline,"v") !=0){
+     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
+     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
+     return 1;
+   }
+   trimbb(resultsav, resultline);
+   if (strlen(resultsav) >1){
+     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
+   }
+   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 variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+   }
+   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 ' '
+                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+     }else
+       cutl(strc,strd,resultsav,'=');
+     Tvalsel[k]=atof(strc); /* 1 */
+     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
+     Tvarsel[k]=atoi(strc);
+     /* 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 */
+   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           match=1;
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       }
+     }
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+     match=0;
+     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       if(Typevar[k1]==0){ /* Single */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+           resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           ++match;
+         }
+       }
+     }
+     if(match == 0){
+       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+     }else if(match > 1){
+       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+     }
+   }
+   /* 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 */
+   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
+   /* 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 */
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=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++){ /* model line */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
+       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
+       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
+       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
+       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
+       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }
+   }
+   TKresult[nres]=++k; /* Combination for the nresult and the model */
+   return (0);
+ }
+ int decodemodel( char model[], int lastobs)
+  /**< This routine decodes the model and returns:
+         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+         * - nagesqr = 1 if age*age in the model, otherwise 0.
+         * - 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
+         * - cptcovs number of simple covariates
+         * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+         *     which is a new column after the 9 (ncovcol) variables.
+         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+         */
+ {
+   int i, j, k, ks, v;
+   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;
+     if (strstr(model,"AGE") !=0){
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
+       return 1;
+     }
+     if (strstr(model,"v") !=0){
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
+     }
+     strcpy(modelsav,model);
+     if ((strpt=strstr(model,"age*age")) !=0){
+       printf(" strpt=%s, model=%s\n",strpt, model);
+       if(strpt != model){
+         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+  corresponding column of parameters.\n",model);
+         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+  corresponding column of parameters.\n",model); fflush(ficlog);
+         return 1;
+       }
+       nagesqr=1;
+       if (strstr(model,"+age*age") !=0)
+         substrchaine(modelsav, model, "+age*age");
+       else if (strstr(model,"age*age+") !=0)
+         substrchaine(modelsav, model, "age*age+");
+       else
+         substrchaine(modelsav, model, "age*age");
+     }else
+       nagesqr=0;
+     if (strlen(modelsav) >1){
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
+       cptcovt= j+1; /* Number of total covariates in the model, not including
+                      * cst, age and age*age
+                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=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  */
+       /*   Design
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+        *  <          ncovcol=8                >
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+        *   k=  1    2      3       4     5       6      7        8
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+        *  covar[k,i], value of kth covariate if not including age for individual i:
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+        *  Tage[++cptcovage]=k
+        *       if products, new covar are created after ncovcol with k1
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+        *  <          ncovcol=8                >
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tprod[1]@2={                         6, 5}
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+        *How to reorganize?
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
+        * Struct []
+        */
+       /* This loop fills the array Tvar from the string 'model'.*/
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
+       /*        k=1 Tvar[1]=2 (from V2) */
+       /*        k=5 Tvar[5] */
+       /* for (k=1; k<=cptcovn;k++) { */
+       /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       /*        } */
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
+       /*
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
+         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
+       }
+       cptcovage=0;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*scanf("%d",i);*/
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+             /* covar is not filled and then is empty */
+             cptcovprod--;
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             Typevar[k]=1;  /* 1 for age product */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             /*printf("stre=%s ", stre);*/
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+             cptcovprod--;
+             cutl(stre,strb,strc,'V');
+             Tvar[k]=atoi(stre);
+             Typevar[k]=1;  /* 1 for age product */
+             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
+                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+             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; /* Tpsprod[3]=1, Tposprod[2]=5 */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][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 { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates 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);
+      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      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        1
+    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=%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=%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;
+       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];
+       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];
+       TvarsQind[nsq]=k;
+       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;
+       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];
+       TvarsQind[nsq]=k;
+       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: ");
+   return (1);
+ }
+ 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;
+         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 + 1;
+         if(firstone == 0){
+           firstone=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)++;
+         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 (#%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]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
+       if(s[m][i] >0  || s[m][i]==-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((int)moisdc[i]!=99 && (int)andc[i]!=9999){
+               agev[m][i]=agedc[i];
+               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             }else {
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 agev[m][i]=-1;
+               }
+             }
+           } /* 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]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
+           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
+         } /* 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 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)++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 1;
+       }
+     }
+   }
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
+ }*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   return (0);
+  /* endread:*/
+     printf("Exiting calandcheckages: ");
+     return (1);
+ }
+ #if defined(_MSC_VER)
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ //#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__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    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..
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
+ #endif
+ /*  __MINGW32__   */
+ /*  __CYGWIN__   */
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
+ /* _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. */
+ #if UINTPTR_MAX == 0xffffffff
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
+ #endif
+ #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) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #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) --------------*/
+   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 */
+       if(i1 != 1 && TKresult[nres]!= k)
+         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<=cptcoveff ;j++) {/* all covariates */
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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++){ */
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+         fprintf(ficrespl,"%.0f ",age );
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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 */
+     } /* cptcov */
+   } /* nres */
+   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,j)]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[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,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,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 ------------*/
+   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 */
+     for(k=1; k<=i1;k++){
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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 ------------*/
+   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 */
+     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<=cptcoveff;j++)
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[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); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+         /*        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);
+         /* 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]);
+           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 *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, 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=0.;
+   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
+   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
+   double fret;
+   double dum=0.; /* Dummy variable */
+   double ***p3mat;
+   /* double ***mobaverage; */
+   char line[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+   char  modeltemp[MAXLINE];
+   char resultline[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
+   int c,  h , cpt, c2;
+   int jl=0;
+   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 */
+   int backcast=0; /* defined as global for mlikeli and mle*/
+   int mobilav=0,popforecast=0;
+   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=0., agebase=0.;
+   double ftolpl=FTOL;
+   double **prlim;
+   double **bprlim;
+   double ***param; /* Matrix of parameters */
+   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;
+   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
+   double **ximort;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+   int *dcwave;
+   char z[1]="c";
+   /*char  *strt;*/
+   char strtend[80];
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
+   /*tml = *localtime(&start_time.tm_sec);*/
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
+   getcwd(pathcd, size);
+ #endif
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
+     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(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+     }
+     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);
+       strcpy (pathtot, val);
+       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);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #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 */
+ #endif
+   printf("Current directory %s!\n",pathcd);
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     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); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
+   /*-------- arguments in the command line --------*/
+   /* Main Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   syscompilerinfo(1);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
+   /* */
+   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 */
+   /* Main ---------arguments file --------*/
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fflush(ficlog);
+     /* goto end; */
+     exit(70);
+   }
+   strcpy(filereso,"o");
+   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;
+   /* Is it a BOM UTF-8 Windows file? */
+   /* First parameter line */
+   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)
+     {
+       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++;
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     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;
+   }
+   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){
+     if (num_filled != 11) {
+       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("but line=%s\n",line);
+       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,"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' %s\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %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);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   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,age*age makes 3*/
+   else
+     ncovmodel=2; /* Constant and age */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+ /* 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 chose 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 */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You chose 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{ /* Begin of mle != -1 or -5 */
+     /* Read guessed parameters */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     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 != 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);
+           exit(1);
+         }
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
+           printf("%1d%1d",i,jj);
+         fprintf(ficlog,"%1d%1d",i,jj);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads parameters values */
+     p=param[1][1];
+     pstart=paramstart[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ( (i1-i) * (j1-j) != 0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads covariance matrix */
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     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++){
+       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
+       if(count != 3){
+         printf("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);
+         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){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
+       fscanf(ficpar,"\n");
+       numlinepar++;
+       if(mle==1)
+                                 printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
+     }
+     /* 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];
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     fflush(ficlog);
+   }    /* End of mle != -3 */
+   /*  Main data
+    */
+   nobs=lastobs-firstobs+1; /* was = lastobs;*/
+   /* num=lvector(1,n); */
+   /* moisnais=vector(1,n); */
+   /* annais=vector(1,n); */
+   /* moisdc=vector(1,n); */
+   /* andc=vector(1,n); */
+   /* weight=vector(1,n); */
+   /* agedc=vector(1,n); */
+   /* cod=ivector(1,n); */
+   /* for(i=1;i<=n;i++){ */
+   num=lvector(firstobs,lastobs);
+   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 */
+   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
+         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); /*  */
+   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.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the 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) */
+   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
+                       */
+   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) /* 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){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,firstobs,lastobs);
+   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(andc,1,n); */
+   /* */
+   wav=ivector(1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   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 */
+   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);
+   cptcoveff=0;
+   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]; */
+   }
+   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).
+    */
+   h=0;
+   /*if (cptcovn > 0) */
+   m=pow(2,cptcoveff);
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            * For k=4 covariates, h goes from 1 to m=2**k
+            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
+            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+            *     h\k   1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     2
+            *    10     2     1     1     2
+            *    11 i=6 1     2     1     2
+            *    12     2     2     1     2
+            *    13 i=7 1 i=4 1     2     2
+            *    14     2     1     2     2
+            *    15 i=8 1     2     2     2
+            *    16     2     2     2     2
+            */
+   /* 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 ?
+      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
+      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
+      * In order to get the real value in the data, we use nbcode
+      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
+      * 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.
+      * #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
+      *              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);
+   /* Initialisation of ----------- gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-MORT_");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# IMaCh-%s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /* Initialisation of --------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-MORT_");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<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-2013-2016-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>  \
+ <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=1+age+%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+ #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, 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,"<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>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+   imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /* For mortality only */
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+     for(i=1;i<=NDIM;i++)
+       for(j=1;j<=NDIM;j++)
+         ximort[i][j]=0.;
+     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     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++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     /*printf("%lf %lf", p[1], p[2]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #else
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"POW-MORT_");
+     strcat(filerespow,fileresu);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #else
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+     /*     gsl_vector_set(x, 0, 0.0268); */
+     /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, 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];
+     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]);
+                                 fprintf(ficlog,"%f ",matcov[i][j]);
+       }
+       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++) {
+       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);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+                 ageminpar=50;
+                 agemaxpar=100;
+     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(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+     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 mortality only */
+   /* Standard  */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
+     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");
+     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);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     /*--------- results files --------------*/
+     /* 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");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\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, 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");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[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 W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     /*  */
+     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");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     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) /* 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\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.7e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while(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);
+         continue;
+       }else
+         break;
+     }
+     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+     /*   ungetc(c,ficpar); */
+     /*   fgets(line, MAXLINE, ficpar); */
+     /*   fputs(line,stdout); */
+     /*   fputs(line,ficparo); */
+     /* } */
+     /* ungetc(c,ficpar); */
+     estepm=0;
+     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;
+       fage = agemaxpar;
+     }
+     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 ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
+     /* Other stuffs, more or less useful */
+     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);
+         continue;
+       }else
+         break;
+     }
+     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){
+       if (num_filled != 7) {
+         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);
+         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);
+         goto end;
+       }
+       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(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       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);
+     }
+     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);
+         continue;
+       }else
+         break;
+     }
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
+       if (num_filled != 1) {
+         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);
+         goto end;
+       }
+       printf("pop_based=%d\n",popbased);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
+       fprintf(ficres,"pop_based=%d\n",popbased);
+     }
+     /* Results */
+     nresult=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=14;
+       }else if (line[0] == '#') {
+         /* If line starts with a # it is a comment */
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         continue;
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
+         parameterline=11;
+       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+         parameterline=13;
+       else{
+         parameterline=14;
+       }
+       switch (parameterline){
+       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){
+           if (num_filled != 8) {
+             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\n, your line=%s . Probably you are running 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 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           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.;
+         }
+         break;
+       case 12:
+         /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
+         if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
+           if (num_filled != 8) {
+             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           /* day and month of proj2 are not used but only year anproj2.*/
+           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+         }
+         break;
+       case 13:
+         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+           if (num_filled == 0){
+             resultline[0]='\0';
+             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             break;
+           } else if (num_filled != 1){
+             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           }
+           nresult++; /* Sum of resultlines */
+           printf("Result %d: result=%s\n",nresult, resultline);
+           if(nresult > MAXRESULTLINES){
+             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             goto end;
+           }
+           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);
+           break;
+         case 14:
+           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);
+             goto end;
+           }
+           break;
+         default:
+           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); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     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{
+       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
+     }
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
+                  jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
+     /*------------ free_vector  -------------*/
+     /*  chdir(path); */
+     /* 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 */
+     prlim=matrix(1,nlstate,1,nlstate);
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
+     fclose(ficrespl);
+     /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
+     fclose(ficrespij);
+     /* ncovcombmax=  pow(2,cptcoveff); */
+     /*-------------- Variance of one-step probabilities---*/
+     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(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     for(i=AGEINF;i<=AGESUP;i++)
+       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
+         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(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+     }
+     /* Backcasting */
+     if(backcast==1){
+       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+       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);
+       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+       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  Backcasting */
+     /* ------ 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_");
+     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' ...", filerese);fflush(stdout);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
+     pstamp(ficreseij);
+     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,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficreseij,"******\n");
+       printf("******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, 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);
+     /*---------- State-specific expectancies and variances ------------*/
+     strcpy(filerest,"T_");
+     strcat(filerest,fileresu);
+     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); fflush(stdout);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
+     strcpy(fileresstde,"STDE_");
+     strcat(fileresstde,fileresu);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with State specific 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 State-specific 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_");
+     strcat(filerescve,fileresu);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. State-specific 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 State-specific Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"V_");
+     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 State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
+     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;
+       printf("\n#****** Result for:");
+       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficlog,"\n#****** Result for:");
+       for(j=1;j<=cptcoveff;j++){
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficrest,"******\n");
+       fprintf(ficlog,"******\n");
+       printf("******\n");
+       fprintf(ficresstdeij,"\n#****** ");
+       fprintf(ficrescveij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficresstdeij,"******\n");
+       fprintf(ficrescveij,"******\n");
+       fprintf(ficresvij,"\n#****** ");
+       /* pstamp(ficresvij); */
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       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) ");
+         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];
+             }
+           }
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
+           /* printf(" age %4.0f ",age); */
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
+             }
+             epj[nlstate+1] +=epj[j];
+           }
+           /* 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");
+         }
+       } /* End vpopbased */
+       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);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
+     } /* End k selection */
+     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(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
+     free_matrix(anint,1,maxwav,firstobs,lastobs);
+     free_matrix(mint,1,maxwav,firstobs,lastobs);
+     free_ivector(cod,firstobs,lastobs);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0 ||mobilavproj !=0)
+       free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+     free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
+   /* endfree:*/
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
+   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(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_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   /* free_imatrix(codtab,1,100,1,10); */
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\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");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   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));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+ /* Executes gnuplot */
+   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)
+ #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");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   strcpy(pplotcmd,plotcmd);
+   if((outcmd=system(plotcmd)) != 0){
+     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){
+       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') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+ end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: "); fflush(stdout);
+     scanf("%s",z);
+   }
+   printf("End\n");
+   exit(0);
+ }

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