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Diff for /imach/src/imach.c between versions 1.125 and 1.232

-version 1.125, 2006/04/04 15:20:31
+version 1.232, 2016/08/22 14:20:21
  Line 1
  /* $Id$
    $State$
    $Log$
+   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);
-   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 1024 /* Was 256. 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
- #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 AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
- #define TINY 1.0e-20
+ #define AGEBASE 40
+ #define AGEOVERFLOW 1.e20
- static double maxarg1,maxarg2;
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #ifdef _WIN32
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ #define ODIRSEPARATOR '/'
- #define rint(a) floor(a+0.5)
+ #else
+ #define DIRSEPARATOR '/'
- static double sqrarg;
+ #define CHARSEPARATOR "/"
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define ODIRSEPARATOR '\\'
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ #endif
- int agegomp= AGEGOMP;
+ /* $Id$ */
- int imx;
+ /* $State$ */
- int stepm=1;
+ #include "version.h"
- /* Stepm, step in month: minimum step interpolation*/
+ char version[]=__IMACH_VERSION__;
+ char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
- int estepm;
+ char fullversion[]="$Revision$ $Date$";
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char strstart[80];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int m,nb;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- long *num;
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- double **pmmij, ***probs;
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- double *ageexmed,*agecens;
+ int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
- double dateintmean=0;
+ int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- double *weight;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- int **s; /* Status */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- double *agedc, **covar, idx;
+ int ncovf=0; /* Total number of effective fixed covariates (dummy of quantitative) in the model */
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int ncovv=0; /* Total number of effective (wave) varying covariates (dummy of quantitative) in the model */
- double *lsurv, *lpop, *tpop;
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
- double ftolhess; /* Tolerance for computing hessian */
+ int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
+ int ntveff=0; /**< ntveff number of effective time varying variables */
- /**************** split *************************/
+ int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ int cptcov=0; /* Working variable */
- {
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ int npar=NPARMAX;
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ int nlstate=2; /* Number of live states */
-   */
+ int ndeath=1; /* Number of dead states */
-   char  *ss;                            /* pointer */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
-   int   l1, l2;                         /* length counters */
+ int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
+ int popbased=0;
-   l1 = strlen(path );                   /* length of path */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ int *wav; /* Number of waves for this individuual 0 is possible */
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ int maxwav=0; /* Maxim number of waves */
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+                    to the likelihood and the sum of weights (done by funcone)*/
-     /* get current working directory */
+ int mle=1, weightopt=0;
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
-       return( GLOCK_ERROR_GETCWD );
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
-     }
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
-     /* got dirc from getcwd*/
+ int countcallfunc=0;  /* Count the number of calls to func */
-     printf(" DIRC = %s \n",dirc);
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
-   } else {                              /* strip direcotry from path */
-     ss++;                               /* after this, the filename */
+ double jmean=1; /* Mean space between 2 waves */
-     l2 = strlen( ss );                  /* length of filename */
+ double **matprod2(); /* test */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
-     strcpy( name, ss );         /* save file name */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
-     dirc[l1-l2] = 0;                    /* add zero */
-     printf(" DIRC2 = %s \n",dirc);
+ /*FILE *fic ; */ /* Used in readdata only */
-   }
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
-   /* We add a separator at the end of dirc if not exists */
+ FILE *ficlog, *ficrespow;
-   l1 = strlen( dirc );                  /* length of directory */
+ int globpr=0; /* Global variable for printing or not */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ double fretone; /* Only one call to likelihood */
-     dirc[l1] =  DIRSEPARATOR;
+ long ipmx=0; /* Number of contributions */
-     dirc[l1+1] = 0;
+ double sw; /* Sum of weights */
-     printf(" DIRC3 = %s \n",dirc);
+ char filerespow[FILENAMELENGTH];
-   }
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
-   ss = strrchr( name, '.' );            /* find last / */
+ FILE *ficresilk;
-   if (ss >0){
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
-     ss++;
+ FILE *ficresprobmorprev;
-     strcpy(ext,ss);                     /* save extension */
+ FILE *fichtm, *fichtmcov; /* Html File */
-     l1= strlen( name);
+ FILE *ficreseij;
-     l2= strlen(ss)+1;
+ char filerese[FILENAMELENGTH];
-     strncpy( finame, name, l1-l2);
+ FILE *ficresstdeij;
-     finame[l1-l2]= 0;
+ char fileresstde[FILENAMELENGTH];
-   }
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
-   return( 0 );                          /* we're done */
+ FILE  *ficresvij;
- }
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- /******************************************/
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
- void replace_back_to_slash(char *s, char*t)
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- {
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
-   int i;
+ char command[FILENAMELENGTH];
-   int lg=0;
+ int  outcmd=0;
-   i=0;
-   lg=strlen(t);
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-   for(i=0; i<= lg; i++) {
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
-     (s[i] = t[i]);
+ char filelog[FILENAMELENGTH]; /* Log file */
-     if (t[i]== '\\') s[i]='/';
+ char filerest[FILENAMELENGTH];
-   }
+ char fileregp[FILENAMELENGTH];
- }
+ char popfile[FILENAMELENGTH];
- int nbocc(char *s, char occ)
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- {
-   int i,j=0;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
-   int lg=20;
+ /* struct timezone tzp; */
-   i=0;
+ /* extern int gettimeofday(); */
-   lg=strlen(s);
+ struct tm tml, *gmtime(), *localtime();
-   for(i=0; i<= lg; i++) {
-   if  (s[i] == occ ) j++;
+ extern time_t time();
-   }
-   return j;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- }
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
+ struct tm tm;
- void cutv(char *u,char *v, char*t, char occ)
- {
+ char strcurr[80], strfor[80];
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ char *endptr;
-      gives u="abcedf" and v="ghi2j" */
+ long lval;
-   int i,lg,j,p=0;
+ double dval;
-   i=0;
-   for(j=0; j<=strlen(t)-1; j++) {
+ #define NR_END 1
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ #define FREE_ARG char*
-   }
+ #define FTOL 1.0e-10
-   lg=strlen(t);
+ #define NRANSI
-   for(j=0; j<p; j++) {
+ #define ITMAX 200
-     (u[j] = t[j]);
-   }
+ #define TOL 2.0e-4
-      u[p]='\0';
+ #define CGOLD 0.3819660
-    for(j=0; j<= lg; j++) {
+ #define ZEPS 1.0e-10
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-   }
- }
+ #define GOLD 1.618034
+ #define GLIMIT 100.0
- /********************** nrerror ********************/
+ #define TINY 1.0e-20
- void nrerror(char error_text[])
+ static double maxarg1,maxarg2;
- {
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-   fprintf(stderr,"ERREUR ...\n");
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-   fprintf(stderr,"%s\n",error_text);
-   exit(EXIT_FAILURE);
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
- }
+ #define rint(a) floor(a+0.5)
- /*********************** vector *******************/
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
- double *vector(int nl, int nh)
+ #define mytinydouble 1.0e-16
- {
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-   double *v;
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ /* static double dsqrarg; */
-   if (!v) nrerror("allocation failure in vector");
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-   return v-nl+NR_END;
+ static double sqrarg;
- }
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- /************************ free vector ******************/
+ int agegomp= AGEGOMP;
- void free_vector(double*v, int nl, int nh)
- {
+ int imx;
-   free((FREE_ARG)(v+nl-NR_END));
+ int stepm=1;
- }
+ /* Stepm, step in month: minimum step interpolation*/
- /************************ivector *******************************/
+ int estepm;
- int *ivector(long nl,long nh)
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- {
-   int *v;
+ int m,nb;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ long *num;
-   if (!v) nrerror("allocation failure in ivector");
+ int firstpass=0, lastpass=4,*cod, *cens;
-   return v-nl+NR_END;
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
- }
+                    covariate for which somebody answered excluding
+                    undefined. Usually 2: 0 and 1. */
- /******************free ivector **************************/
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
- void free_ivector(int *v, long nl, long nh)
+                              covariate for which somebody answered including
- {
+                              undefined. Usually 3: -1, 0 and 1. */
-   free((FREE_ARG)(v+nl-NR_END));
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- }
+ double **pmmij, ***probs; /* Global pointer */
+ double ***mobaverage, ***mobaverages; /* New global variable */
- /************************lvector *******************************/
+ double *ageexmed,*agecens;
- long *lvector(long nl,long nh)
+ double dateintmean=0;
- {
-   long *v;
+ double *weight;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ int **s; /* Status */
-   if (!v) nrerror("allocation failure in ivector");
+ double *agedc;
-   return v-nl+NR_END;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
- }
+                   * covar=matrix(0,NCOVMAX,1,n);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
- /******************free lvector **************************/
+ double **coqvar; /* Fixed quantitative covariate iqv */
- void free_lvector(long *v, long nl, long nh)
+ double ***cotvar; /* Time varying covariate itv */
- {
+ double ***cotqvar; /* Time varying quantitative covariate itqv */
-   free((FREE_ARG)(v+nl-NR_END));
+ double  idx;
- }
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ 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 */
- /******************* imatrix *******************************/
+ 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 **imatrix(long nrl, long nrh, long ncl, long nch)
+ 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 */
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
- {
+ int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-   int **m;
+ 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 */
-   /* allocate pointers to rows */
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ 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 += NR_END;
+ int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-   m -= nrl;
+ int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
-   /* allocate rows and set pointers to them */
+ int *Tvarsel; /**< Selected covariates for output */
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ double *Tvalsel; /**< Selected modality value of covariate for output */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
-   m[nrl] += NR_END;
+ int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
-   m[nrl] -= ncl;
+ int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *Tage;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ 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*/
-   /* return pointer to array of pointers to rows */
+ 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*/
-   return m;
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
- }
+ int *Ndum; /** Freq of modality (tricode */
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
- /****************** free_imatrix *************************/
+ int **Tvard;
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ int *Tprod;/**< Gives the k position of the k1 product */
-       int **m;
+ int *Tposprod; /**< Gives the k1 product from the k position */
-       long nch,ncl,nrh,nrl;
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-      /* free an int matrix allocated by imatrix() */
+    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
- {
+    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ */
-   free((FREE_ARG) (m+nrl-NR_END));
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
- }
+ double *lsurv, *lpop, *tpop;
- /******************* matrix *******************************/
+ #define FD 1; /* Fixed dummy covariate */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+ #define FQ 2; /* Fixed quantitative covariate */
- {
+ #define FP 3; /* Fixed product covariate */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
-   double **m;
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ #define VD 10; /* Varying dummy covariate */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ #define VQ 11; /* Varying quantitative covariate */
-   m += NR_END;
+ #define VP 12; /* Varying product covariate */
-   m -= nrl;
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ #define APFD 16; /* Age product * fixed dummy covariate */
-   m[nrl] += NR_END;
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
-   m[nrl] -= ncl;
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   return m;
+ #define FTYPE 1; /* Fixed covariate */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
-    */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
- }
+ struct kmodel{
- /*************************free matrix ************************/
+         int maintype; /* main type */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+         int subtype; /* subtype */
- {
+ };
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ struct kmodel modell[NCOVMAX];
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+ double ftolhess; /**< Tolerance for computing hessian */
- /******************* ma3x *******************************/
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /**************** split *************************/
- {
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ {
-   double ***m;
+   /* 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)
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   char  *ss;                            /* pointer */
-   m += NR_END;
+   int   l1=0, l2=0;                             /* length counters */
-   m -= nrl;
+   l1 = strlen(path );                   /* length of path */
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   m[nrl] += NR_END;
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   m[nrl] -= ncl;
+     strcpy( name, path );               /* we got the fullname name because no directory */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+     /* get current working directory */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ #ifdef WIN32
-   m[nrl][ncl] += NR_END;
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   m[nrl][ncl] -= nll;
+ #else
-   for (j=ncl+1; j<=nch; j++)
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ #endif
+       return( GLOCK_ERROR_GETCWD );
-   for (i=nrl+1; i<=nrh; i++) {
+     }
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+     /* got dirc from getcwd*/
-     for (j=ncl+1; j<=nch; j++)
+     printf(" DIRC = %s \n",dirc);
-       m[i][j]=m[i][j-1]+nlay;
+   } else {                              /* strip directory from path */
-   }
+     ss++;                               /* after this, the filename */
-   return m;
+     l2 = strlen( ss );                  /* length of filename */
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+     strcpy( name, ss );         /* save file name */
-   */
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
- }
+     dirc[l1-l2] = '\0';                 /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
- /*************************free ma3x ************************/
+   }
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   /* We add a separator at the end of dirc if not exists */
- {
+   l1 = strlen( dirc );                  /* length of directory */
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+     dirc[l1] =  DIRSEPARATOR;
-   free((FREE_ARG)(m+nrl-NR_END));
+     dirc[l1+1] = 0;
- }
+     printf(" DIRC3 = %s \n",dirc);
+   }
- /*************** function subdirf ***********/
+   ss = strrchr( name, '.' );            /* find last / */
- char *subdirf(char fileres[])
+   if (ss >0){
- {
+     ss++;
-   /* Caution optionfilefiname is hidden */
+     strcpy(ext,ss);                     /* save extension */
-   strcpy(tmpout,optionfilefiname);
+     l1= strlen( name);
-   strcat(tmpout,"/"); /* Add to the right */
+     l2= strlen(ss)+1;
-   strcat(tmpout,fileres);
+     strncpy( finame, name, l1-l2);
-   return tmpout;
+     finame[l1-l2]= 0;
- }
+   }
- /*************** function subdirf2 ***********/
+   return( 0 );                          /* we're done */
- char *subdirf2(char fileres[], char *preop)
+ }
- {
-   /* Caution optionfilefiname is hidden */
+ /******************************************/
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+ void replace_back_to_slash(char *s, char*t)
-   strcat(tmpout,preop);
+ {
-   strcat(tmpout,fileres);
+   int i;
-   return tmpout;
+   int lg=0;
- }
+   i=0;
+   lg=strlen(t);
- /*************** function subdirf3 ***********/
+   for(i=0; i<= lg; i++) {
- char *subdirf3(char fileres[], char *preop, char *preop2)
+     (s[i] = t[i]);
- {
+     if (t[i]== '\\') s[i]='/';
+   }
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+ char *trimbb(char *out, char *in)
-   strcat(tmpout,preop);
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   strcat(tmpout,preop2);
+   char *s;
-   strcat(tmpout,fileres);
+   s=out;
-   return tmpout;
+   while (*in != '\0'){
- }
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
- /***************** f1dim *************************/
+     }
- extern int ncom;
+     *out++ = *in++;
- extern double *pcom,*xicom;
+   }
- extern double (*nrfunc)(double []);
+   *out='\0';
+   return s;
- double f1dim(double x)
+ }
- {
-   int j;
+ /* char *substrchaine(char *out, char *in, char *chain) */
-   double f;
+ /* { */
-   double *xt;
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+ /*   char *s, *t; */
-   xt=vector(1,ncom);
+ /*   t=in;s=out; */
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ /*   while ((*in != *chain) && (*in != '\0')){ */
-   f=(*nrfunc)(xt);
+ /*     *out++ = *in++; */
-   free_vector(xt,1,ncom);
+ /*   } */
-   return f;
- }
+ /*   /\* *in matches *chain *\/ */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
- /*****************brent *************************/
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+ /*   } */
- {
+ /*   in--; chain--; */
-   int iter;
+ /*   while ( (*in != '\0')){ */
-   double a,b,d,etemp;
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-   double fu,fv,fw,fx;
+ /*     *out++ = *in++; */
-   double ftemp;
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ /*   } */
-   double e=0.0;
+ /*   *out='\0'; */
+ /*   out=s; */
-   a=(ax < cx ? ax : cx);
+ /*   return out; */
-   b=(ax > cx ? ax : cx);
+ /* } */
-   x=w=v=bx;
+ char *substrchaine(char *out, char *in, char *chain)
-   fw=fv=fx=(*f)(x);
+ {
-   for (iter=1;iter<=ITMAX;iter++) {
+   /* Substract chain 'chain' from 'in', return and output 'out' */
-     xm=0.5*(a+b);
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   char *strloc;
-     printf(".");fflush(stdout);
-     fprintf(ficlog,".");fflush(ficlog);
+   strcpy (out, in);
- #ifdef DEBUG
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
-     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);
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   if(strloc != NULL){
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
- #endif
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+     /* strcpy (strloc, strloc +strlen(chain));*/
-       *xmin=x;
+   }
-       return fx;
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
-     }
+   return out;
-     ftemp=fu;
+ }
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
-       q=(x-v)*(fx-fw);
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-       p=(x-v)*q-(x-w)*r;
+ {
-       q=2.0*(q-r);
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
-       if (q > 0.0) p = -p;
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-       q=fabs(q);
+      gives blocc="abcdef" and alocc="ghi2j".
-       etemp=e;
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-       e=d;
+   */
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   char *s, *t;
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   t=in;s=in;
-       else {
+   while ((*in != occ) && (*in != '\0')){
-         d=p/q;
+     *alocc++ = *in++;
-         u=x+d;
+   }
-         if (u-a < tol2 || b-u < tol2)
+   if( *in == occ){
-           d=SIGN(tol1,xm-x);
+     *(alocc)='\0';
-       }
+     s=++in;
-     } else {
+   }
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+   if (s == t) {/* occ not found */
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+     *(alocc-(in-s))='\0';
-     fu=(*f)(u);
+     in=s;
-     if (fu <= fx) {
+   }
-       if (u >= x) a=x; else b=x;
+   while ( *in != '\0'){
-       SHFT(v,w,x,u)
+     *blocc++ = *in++;
-         SHFT(fv,fw,fx,fu)
+   }
-         } else {
-           if (u < x) a=u; else b=u;
+   *blocc='\0';
-           if (fu <= fw || w == x) {
+   return t;
-             v=w;
+ }
-             w=u;
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-             fv=fw;
+ {
-             fw=fu;
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
-           } else if (fu <= fv || v == x || v == w) {
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-             v=u;
+      gives blocc="abcdef2ghi" and alocc="j".
-             fv=fu;
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-           }
+   */
-         }
+   char *s, *t;
-   }
+   t=in;s=in;
-   nrerror("Too many iterations in brent");
+   while (*in != '\0'){
-   *xmin=x;
+     while( *in == occ){
-   return fx;
+       *blocc++ = *in++;
- }
+       s=in;
+     }
- /****************** mnbrak ***********************/
+     *blocc++ = *in++;
+   }
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   if (s == t) /* occ not found */
-             double (*func)(double))
+     *(blocc-(in-s))='\0';
- {
+   else
-   double ulim,u,r,q, dum;
+     *(blocc-(in-s)-1)='\0';
-   double fu;
+   in=s;
+   while ( *in != '\0'){
-   *fa=(*func)(*ax);
+     *alocc++ = *in++;
-   *fb=(*func)(*bx);
+   }
-   if (*fb > *fa) {
-     SHFT(dum,*ax,*bx,dum)
+   *alocc='\0';
-       SHFT(dum,*fb,*fa,dum)
+   return s;
-       }
+ }
-   *cx=(*bx)+GOLD*(*bx-*ax);
-   *fc=(*func)(*cx);
+ int nbocc(char *s, char occ)
-   while (*fb > *fc) {
+ {
-     r=(*bx-*ax)*(*fb-*fc);
+   int i,j=0;
-     q=(*bx-*cx)*(*fb-*fa);
+   int lg=20;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   i=0;
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   lg=strlen(s);
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   for(i=0; i<= lg; i++) {
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   if  (s[i] == occ ) j++;
-       fu=(*func)(u);
+   }
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+   return j;
-       fu=(*func)(u);
+ }
-       if (fu < *fc) {
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ /* void cutv(char *u,char *v, char*t, char occ) */
-           SHFT(*fb,*fc,fu,(*func)(u))
+ /* { */
-           }
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-       u=ulim;
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-       fu=(*func)(u);
+ /*   int i,lg,j,p=0; */
-     } else {
+ /*   i=0; */
-       u=(*cx)+GOLD*(*cx-*bx);
+ /*   lg=strlen(t); */
-       fu=(*func)(u);
+ /*   for(j=0; j<=lg-1; j++) { */
-     }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-     SHFT(*ax,*bx,*cx,u)
+ /*   } */
-       SHFT(*fa,*fb,*fc,fu)
-       }
+ /*   for(j=0; j<p; j++) { */
- }
+ /*     (u[j] = t[j]); */
+ /*   } */
- /*************** linmin ************************/
+ /*      u[p]='\0'; */
- int ncom;
+ /*    for(j=0; j<= lg; j++) { */
- double *pcom,*xicom;
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
- double (*nrfunc)(double []);
+ /*   } */
+ /* } */
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
- {
+ #ifdef _WIN32
-   double brent(double ax, double bx, double cx,
+ char * strsep(char **pp, const char *delim)
-                double (*f)(double), double tol, double *xmin);
+ {
-   double f1dim(double x);
+   char *p, *q;
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-               double *fc, double (*func)(double));
+   if ((p = *pp) == NULL)
-   int j;
+     return 0;
-   double xx,xmin,bx,ax;
+   if ((q = strpbrk (p, delim)) != NULL)
-   double fx,fb,fa;
+   {
+     *pp = q + 1;
-   ncom=n;
+     *q = '\0';
-   pcom=vector(1,n);
+   }
-   xicom=vector(1,n);
+   else
-   nrfunc=func;
+     *pp = 0;
-   for (j=1;j<=n;j++) {
+   return p;
-     pcom[j]=p[j];
+ }
-     xicom[j]=xi[j];
+ #endif
-   }
-   ax=0.0;
+ /********************** nrerror ********************/
-   xx=1.0;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ void nrerror(char error_text[])
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ {
- #ifdef DEBUG
+   fprintf(stderr,"ERREUR ...\n");
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(stderr,"%s\n",error_text);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   exit(EXIT_FAILURE);
- #endif
+ }
-   for (j=1;j<=n;j++) {
+ /*********************** vector *******************/
-     xi[j] *= xmin;
+ double *vector(int nl, int nh)
-     p[j] += xi[j];
+ {
-   }
+   double *v;
-   free_vector(xicom,1,n);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   free_vector(pcom,1,n);
+   if (!v) nrerror("allocation failure in vector");
- }
+   return v-nl+NR_END;
+ }
- char *asc_diff_time(long time_sec, char ascdiff[])
- {
+ /************************ free vector ******************/
-   long sec_left, days, hours, minutes;
+ void free_vector(double*v, int nl, int nh)
-   days = (time_sec) / (60*60*24);
+ {
-   sec_left = (time_sec) % (60*60*24);
+   free((FREE_ARG)(v+nl-NR_END));
-   hours = (sec_left) / (60*60) ;
+ }
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
+ /************************ivector *******************************/
-   sec_left = (sec_left) % (60);
+ int *ivector(long nl,long nh)
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ {
-   return ascdiff;
+   int *v;
- }
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   if (!v) nrerror("allocation failure in ivector");
- /*************** powell ************************/
+   return v-nl+NR_END;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+ }
-             double (*func)(double []))
- {
+ /******************free ivector **************************/
-   void linmin(double p[], double xi[], int n, double *fret,
+ void free_ivector(int *v, long nl, long nh)
-               double (*func)(double []));
+ {
-   int i,ibig,j;
+   free((FREE_ARG)(v+nl-NR_END));
-   double del,t,*pt,*ptt,*xit;
+ }
-   double fp,fptt;
-   double *xits;
+ /************************lvector *******************************/
-   int niterf, itmp;
+ long *lvector(long nl,long nh)
+ {
-   pt=vector(1,n);
+   long *v;
-   ptt=vector(1,n);
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   xit=vector(1,n);
+   if (!v) nrerror("allocation failure in ivector");
-   xits=vector(1,n);
+   return v-nl+NR_END;
-   *fret=(*func)(p);
+ }
-   for (j=1;j<=n;j++) pt[j]=p[j];
-   for (*iter=1;;++(*iter)) {
+ /******************free lvector **************************/
-     fp=(*fret);
+ void free_lvector(long *v, long nl, long nh)
-     ibig=0;
+ {
-     del=0.0;
+   free((FREE_ARG)(v+nl-NR_END));
-     last_time=curr_time;
+ }
-     (void) gettimeofday(&curr_time,&tzp);
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+ /******************* imatrix *******************************/
-     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);
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-    for (i=1;i<=n;i++) {
+ {
-       printf(" %d %.12f",i, p[i]);
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   int **m;
-       fprintf(ficrespow," %.12lf", p[i]);
-     }
+   /* allocate pointers to rows */
-     printf("\n");
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-     fprintf(ficlog,"\n");
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   m += NR_END;
-     if(*iter <=3){
+   m -= nrl;
-       tm = *localtime(&curr_time.tv_sec);
-       strcpy(strcurr,asctime(&tm));
- /*       asctime_r(&tm,strcurr); */
+   /* allocate rows and set pointers to them */
-       forecast_time=curr_time;
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-       itmp = strlen(strcurr);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   m[nrl] += NR_END;
-         strcurr[itmp-1]='\0';
+   m[nrl] -= ncl;
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-       for(niterf=10;niterf<=30;niterf+=10){
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+   /* return pointer to array of pointers to rows */
-         tmf = *localtime(&forecast_time.tv_sec);
+   return m;
- /*      asctime_r(&tmf,strfor); */
+ }
-         strcpy(strfor,asctime(&tmf));
-         itmp = strlen(strfor);
+ /****************** free_imatrix *************************/
-         if(strfor[itmp-1]=='\n')
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-         strfor[itmp-1]='\0';
+       int **m;
-         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 nch,ncl,nrh,nrl;
-         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);
+      /* free an int matrix allocated by imatrix() */
-       }
+ {
-     }
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     for (i=1;i<=n;i++) {
+   free((FREE_ARG) (m+nrl-NR_END));
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+ }
-       fptt=(*fret);
- #ifdef DEBUG
+ /******************* matrix *******************************/
-       printf("fret=%lf \n",*fret);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       fprintf(ficlog,"fret=%lf \n",*fret);
+ {
- #endif
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-       printf("%d",i);fflush(stdout);
+   double **m;
-       fprintf(ficlog,"%d",i);fflush(ficlog);
-       linmin(p,xit,n,fret,func);
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       if (fabs(fptt-(*fret)) > del) {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-         del=fabs(fptt-(*fret));
+   m += NR_END;
-         ibig=i;
+   m -= nrl;
-       }
- #ifdef DEBUG
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       printf("%d %.12e",i,(*fret));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   m[nrl] += NR_END;
-       for (j=1;j<=n;j++) {
+   m[nrl] -= ncl;
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf(" x(%d)=%.12e",j,xit[j]);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   return m;
-       }
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-       for(j=1;j<=n;j++) {
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-         printf(" p=%.12e",p[j]);
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-         fprintf(ficlog," p=%.12e",p[j]);
+    */
-       }
+ }
-       printf("\n");
-       fprintf(ficlog,"\n");
+ /*************************free matrix ************************/
- #endif
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-     }
+ {
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- #ifdef DEBUG
+   free((FREE_ARG)(m+nrl-NR_END));
-       int k[2],l;
+ }
-       k[0]=1;
-       k[1]=-1;
+ /******************* ma3x *******************************/
-       printf("Max: %.12e",(*func)(p));
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+ {
-       for (j=1;j<=n;j++) {
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-         printf(" %.12e",p[j]);
+   double ***m;
-         fprintf(ficlog," %.12e",p[j]);
-       }
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       printf("\n");
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       fprintf(ficlog,"\n");
+   m += NR_END;
-       for(l=0;l<=1;l++) {
+   m -= nrl;
-         for (j=1;j<=n;j++) {
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   m[nrl] += NR_END;
-         }
+   m[nrl] -= ncl;
-         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)));
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-       }
- #endif
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   m[nrl][ncl] += NR_END;
-       free_vector(xit,1,n);
+   m[nrl][ncl] -= nll;
-       free_vector(xits,1,n);
+   for (j=ncl+1; j<=nch; j++)
-       free_vector(ptt,1,n);
+     m[nrl][j]=m[nrl][j-1]+nlay;
-       free_vector(pt,1,n);
-       return;
+   for (i=nrl+1; i<=nrh; i++) {
-     }
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     for (j=ncl+1; j<=nch; j++)
-     for (j=1;j<=n;j++) {
+       m[i][j]=m[i][j-1]+nlay;
-       ptt[j]=2.0*p[j]-pt[j];
+   }
-       xit[j]=p[j]-pt[j];
+   return m;
-       pt[j]=p[j];
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-     }
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-     fptt=(*func)(ptt);
+   */
-     if (fptt < fp) {
+ }
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-       if (t < 0.0) {
+ /*************************free ma3x ************************/
-         linmin(p,xit,n,fret,func);
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-         for (j=1;j<=n;j++) {
+ {
-           xi[j][ibig]=xi[j][n];
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-           xi[j][n]=xit[j];
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-         }
+   free((FREE_ARG)(m+nrl-NR_END));
- #ifdef DEBUG
+ }
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ /*************** function subdirf ***********/
-         for(j=1;j<=n;j++){
+ char *subdirf(char fileres[])
-           printf(" %.12e",xit[j]);
+ {
-           fprintf(ficlog," %.12e",xit[j]);
+   /* Caution optionfilefiname is hidden */
-         }
+   strcpy(tmpout,optionfilefiname);
-         printf("\n");
+   strcat(tmpout,"/"); /* Add to the right */
-         fprintf(ficlog,"\n");
+   strcat(tmpout,fileres);
- #endif
+   return tmpout;
-       }
+ }
-     }
-   }
+ /*************** function subdirf2 ***********/
- }
+ char *subdirf2(char fileres[], char *preop)
+ {
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   /* Caution optionfilefiname is hidden */
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   strcpy(tmpout,optionfilefiname);
- {
+   strcat(tmpout,"/");
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   strcat(tmpout,preop);
-      matrix by transitions matrix until convergence is reached */
+   strcat(tmpout,fileres);
+   return tmpout;
-   int i, ii,j,k;
+ }
-   double min, max, maxmin, maxmax,sumnew=0.;
-   double **matprod2();
+ /*************** function subdirf3 ***********/
-   double **out, cov[NCOVMAX], **pmij();
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   double **newm;
+ {
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   /* Caution optionfilefiname is hidden */
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   strcpy(tmpout,optionfilefiname);
-     for (j=1;j<=nlstate+ndeath;j++){
+   strcat(tmpout,"/");
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   strcat(tmpout,preop);
-     }
+   strcat(tmpout,preop2);
+   strcat(tmpout,fileres);
-    cov[1]=1.;
+   return tmpout;
+ }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ /*************** function subdirfext ***********/
-     newm=savm;
+ char *subdirfext(char fileres[], char *preop, char *postop)
-     /* Covariates have to be included here again */
+ {
-      cov[2]=agefin;
+   strcpy(tmpout,preop);
-       for (k=1; k<=cptcovn;k++) {
+   strcat(tmpout,fileres);
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   strcat(tmpout,postop);
-         /*      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]]);*/
+   return tmpout;
-       }
+ }
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+ /*************** function subdirfext3 ***********/
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ char *subdirfext3(char fileres[], char *preop, char *postop)
+ {
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+   /* Caution optionfilefiname is hidden */
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   strcpy(tmpout,optionfilefiname);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
-     savm=oldm;
+   strcat(tmpout,fileres);
-     oldm=newm;
+   strcat(tmpout,postop);
-     maxmax=0.;
+   return tmpout;
-     for(j=1;j<=nlstate;j++){
+ }
-       min=1.;
-       max=0.;
+ char *asc_diff_time(long time_sec, char ascdiff[])
-       for(i=1; i<=nlstate; i++) {
+ {
-         sumnew=0;
+   long sec_left, days, hours, minutes;
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+   days = (time_sec) / (60*60*24);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+   sec_left = (time_sec) % (60*60*24);
-         max=FMAX(max,prlim[i][j]);
+   hours = (sec_left) / (60*60) ;
-         min=FMIN(min,prlim[i][j]);
+   sec_left = (sec_left) %(60*60);
-       }
+   minutes = (sec_left) /60;
-       maxmin=max-min;
+   sec_left = (sec_left) % (60);
-       maxmax=FMAX(maxmax,maxmin);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-     }
+   return ascdiff;
-     if(maxmax < ftolpl){
+ }
-       return prlim;
-     }
+ /***************** f1dim *************************/
-   }
+ extern int ncom;
- }
+ extern double *pcom,*xicom;
+ extern double (*nrfunc)(double []);
- /*************** transition probabilities ***************/
+ double f1dim(double x)
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
- {
+   int j;
-   double s1, s2;
+   double f;
-   /*double t34;*/
+   double *xt;
-   int i,j,j1, nc, ii, jj;
+   xt=vector(1,ncom);
-     for(i=1; i<= nlstate; i++){
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-       for(j=1; j<i;j++){
+   f=(*nrfunc)(xt);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+   free_vector(xt,1,ncom);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+   return f;
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ }
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-         }
+ /*****************brent *************************/
-         ps[i][j]=s2;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ {
-       }
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       for(j=i+1; j<=nlstate+ndeath;j++){
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+    * returned function value.
-         }
+   */
-         ps[i][j]=s2;
+   int iter;
-       }
+   double a,b,d,etemp;
-     }
+   double fu=0,fv,fw,fx;
-     /*ps[3][2]=1;*/
+   double ftemp=0.;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-     for(i=1; i<= nlstate; i++){
+   double e=0.0;
-       s1=0;
-       for(j=1; j<i; j++)
+   a=(ax < cx ? ax : cx);
-         s1+=exp(ps[i][j]);
+   b=(ax > cx ? ax : cx);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+   x=w=v=bx;
-         s1+=exp(ps[i][j]);
+   fw=fv=fx=(*f)(x);
-       ps[i][i]=1./(s1+1.);
+   for (iter=1;iter<=ITMAX;iter++) {
-       for(j=1; j<i; j++)
+     xm=0.5*(a+b);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     printf(".");fflush(stdout);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     fprintf(ficlog,".");fflush(ficlog);
-     } /* end i */
+ #ifdef DEBUGBRENT
+     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);
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     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);
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-         ps[ii][jj]=0;
+ #endif
-         ps[ii][ii]=1;
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       }
+       *xmin=x;
-     }
+       return fx;
+     }
+     ftemp=fu;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     if (fabs(e) > tol1) {
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       r=(x-w)*(fx-fv);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       q=(x-v)*(fx-fw);
- /*       } */
+       p=(x-v)*q-(x-w)*r;
- /*       printf("\n "); */
+       q=2.0*(q-r);
- /*        } */
+       if (q > 0.0) p = -p;
- /*        printf("\n ");printf("%lf ",cov[2]); */
+       q=fabs(q);
-        /*
+       etemp=e;
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       e=d;
-       goto end;*/
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-     return ps;
+                                 d=CGOLD*(e=(x >= xm ? a-x : b-x));
- }
+       else {
+                                 d=p/q;
- /**************** Product of 2 matrices ******************/
+                                 u=x+d;
+                                 if (u-a < tol2 || b-u < tol2)
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+                                         d=SIGN(tol1,xm-x);
- {
+       }
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+     } else {
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-   /* in, b, out are matrice of pointers which should have been initialized
+     }
-      before: only the contents of out is modified. The function returns
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-      a pointer to pointers identical to out */
+     fu=(*f)(u);
-   long i, j, k;
+     if (fu <= fx) {
-   for(i=nrl; i<= nrh; i++)
+       if (u >= x) a=x; else b=x;
-     for(k=ncolol; k<=ncoloh; k++)
+       SHFT(v,w,x,u)
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       SHFT(fv,fw,fx,fu)
-         out[i][k] +=in[i][j]*b[j][k];
+     } else {
+       if (u < x) a=u; else b=u;
-   return out;
+       if (fu <= fw || w == x) {
- }
+                                 v=w;
+                                 w=u;
+                                 fv=fw;
- /************* Higher Matrix Product ***************/
+                                 fw=fu;
+       } else if (fu <= fv || v == x || v == w) {
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+                                 v=u;
- {
+                                 fv=fu;
-   /* Computes the transition matrix starting at age 'age' over
+       }
-      'nhstepm*hstepm*stepm' months (i.e. until
+     }
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+   }
-      nhstepm*hstepm matrices.
+   nrerror("Too many iterations in brent");
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+   *xmin=x;
-      (typically every 2 years instead of every month which is too big
+   return fx;
-      for the memory).
+ }
-      Model is determined by parameters x and covariates have to be
-      included manually here.
+ /****************** mnbrak ***********************/
-      */
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+             double (*func)(double))
-   int i, j, d, h, k;
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
-   double **out, cov[NCOVMAX];
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
-   double **newm;
+ 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.
-   /* Hstepm could be zero and should return the unit matrix */
+    */
-   for (i=1;i<=nlstate+ndeath;i++)
+   double ulim,u,r,q, dum;
-     for (j=1;j<=nlstate+ndeath;j++){
+   double fu;
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+   double scale=10.;
-     }
+   int iterscale=0;
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(h=1; h <=nhstepm; h++){
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
-     for(d=1; d <=hstepm; d++){
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
-       newm=savm;
-       /* Covariates have to be included here again */
-       cov[1]=1.;
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-       for (k=1; k<=cptcovage;k++)
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   /* } */
-       for (k=1; k<=cptcovprod;k++)
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   if (*fb > *fa) {
+     SHFT(dum,*ax,*bx,dum)
+     SHFT(dum,*fb,*fa,dum)
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+   }
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+   *fc=(*func)(*cx);
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef DEBUG
-       savm=oldm;
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-       oldm=newm;
+   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-     }
+ #endif
-     for(i=1; i<=nlstate+ndeath; i++)
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
-       for(j=1;j<=nlstate+ndeath;j++) {
+     r=(*bx-*ax)*(*fb-*fc);
-         po[i][j][h]=newm[i][j];
+     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-          */
+       (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 */
-   } /* end h */
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-   return po;
+       fu=(*func)(u);
- }
+ #ifdef DEBUG
+       /* f(x)=A(x-u)**2+f(u) */
+       double A, fparabu;
- /*************** log-likelihood *************/
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
- double func( double *x)
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
- {
+       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);
-   int i, ii, j, k, mi, d, kk;
+       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);
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-   double **out;
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-   double sw; /* Sum of weights */
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-   double lli; /* Individual log likelihood */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-   int s1, s2;
+ #endif
-   double bbh, survp;
+ #ifdef MNBRAKORIGINAL
-   long ipmx;
+ #else
-   /*extern weight */
+ /*       if (fu > *fc) { */
-   /* We are differentiating ll according to initial status */
+ /* #ifdef DEBUG */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ /*       printf("mnbrak4  fu > fc \n"); */
-   /*for(i=1;i<imx;i++)
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
-     printf(" %d\n",s[4][i]);
+ /* #endif */
-   */
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
-   cov[1]=1.;
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+ /*      dum=u; /\* Shifting c and u *\/ */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ /*      u = *cx; */
+ /*      *cx = dum; */
-   if(mle==1){
+ /*      dum = fu; */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ /*      fu = *fc; */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ /*      *fc =dum; */
-       for(mi=1; mi<= wav[i]-1; mi++){
+ /*       } else { /\* end *\/ */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ /* #ifdef DEBUG */
-           for (j=1;j<=nlstate+ndeath;j++){
+ /*       printf("mnbrak3  fu < fc \n"); */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ /* #endif */
-           }
+ /*      dum=u; /\* Shifting c and u *\/ */
-         for(d=0; d<dh[mi][i]; d++){
+ /*      u = *cx; */
-           newm=savm;
+ /*      *cx = dum; */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ /*      dum = fu; */
-           for (kk=1; kk<=cptcovage;kk++) {
+ /*      fu = *fc; */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ /*      *fc =dum; */
-           }
+ /*       } */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ #ifdef DEBUGMNBRAK
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+                  double A, fparabu;
-           savm=oldm;
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-           oldm=newm;
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
-         } /* end mult */
+      printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+      fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+ #endif
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       dum=u; /* Shifting c and u */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+       u = *cx;
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       *cx = dum;
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+       dum = fu;
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+       fu = *fc;
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       *fc =dum;
-          * 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
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-          * -stepm/2 to stepm/2 .
+ #ifdef DEBUG
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
-          * For stepm > 1 the results are less biased than in previous versions.
+       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
-          */
+ #endif
-         s1=s[mw[mi][i]][i];
+       fu=(*func)(u);
-         s2=s[mw[mi+1][i]][i];
+       if (fu < *fc) {
-         bbh=(double)bh[mi][i]/(double)stepm;
+ #ifdef DEBUG
-         /* bias bh is positive if real duration
+                                 printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-          * is higher than the multiple of stepm and negative otherwise.
+                           fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-          */
+ #endif
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+                           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         if( s2 > nlstate){
+                                 SHFT(*fb,*fc,fu,(*func)(u))
-           /* i.e. if s2 is a death state and if the date of death is known
+ #ifdef DEBUG
-              then the contribution to the likelihood is the probability to
+                                         printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
-              die between last step unit time and current  step unit time,
+ #endif
-              which is also equal to probability to die before dh
+       }
-              minus probability to die before dh-stepm .
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-              In version up to 0.92 likelihood was computed
+ #ifdef DEBUG
-         as if date of death was unknown. Death was treated as any other
+       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
-         health state: the date of the interview describes the actual state
+       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
-         and not the date of a change in health state. The former idea was
+ #endif
-         to consider that at each interview the state was recorded
+       u=ulim;
-         (healthy, disable or death) and IMaCh was corrected; but when we
+       fu=(*func)(u);
-         introduced the exact date of death then we should have modified
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
-         the contribution of an exact death to the likelihood. This new
+ #ifdef DEBUG
-         contribution is smaller and very dependent of the step unit
+       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
-         stepm. It is no more the probability to die between last interview
+       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);
-         and month of death but the probability to survive from last
+ #endif
-         interview up to one month before death multiplied by the
+       u=(*cx)+GOLD*(*cx-*bx);
-         probability to die within a month. Thanks to Chris
+       fu=(*func)(u);
-         Jackson for correcting this bug.  Former versions increased
+ #ifdef DEBUG
-         mortality artificially. The bad side is that we add another loop
+       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
-         which slows down the processing. The difference can be up to 10%
+       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
-         lower mortality.
+ #endif
-           */
+     } /* end tests */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+     SHFT(*ax,*bx,*cx,u)
+     SHFT(*fa,*fb,*fc,fu)
+ #ifdef DEBUG
-         } else if  (s2==-2) {
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-           for (j=1,survp=0. ; j<=nlstate; j++)
+       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ #endif
-           /*survp += out[s1][j]; */
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-           lli= log(survp);
+ }
-         }
+ /*************** linmin ************************/
-         else if  (s2==-4) {
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-           for (j=3,survp=0. ; j<=nlstate; j++)
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-           lli= log(survp);
+ the value of func at the returned location p . This is actually all accomplished by calling the
-         }
+ routines mnbrak and brent .*/
+ int ncom;
-         else if  (s2==-5) {
+ double *pcom,*xicom;
-           for (j=1,survp=0. ; j<=2; j++)
+ double (*nrfunc)(double []);
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           lli= log(survp);
+ #ifdef LINMINORIGINAL
-         }
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ #else
-         else{
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ #endif
-           /*  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 brent(double ax, double bx, double cx,
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+                double (*f)(double), double tol, double *xmin);
-         /*if(lli ==000.0)*/
+   double f1dim(double x);
-         /*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); */
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-         ipmx +=1;
+               double *fc, double (*func)(double));
-         sw += weight[i];
+   int j;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   double xx,xmin,bx,ax;
-       } /* end of wave */
+   double fx,fb,fa;
-     } /* end of individual */
-   }  else if(mle==2){
+ #ifdef LINMINORIGINAL
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #else
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   double scale=10., axs, xxs; /* Scale added for infinity */
-       for(mi=1; mi<= wav[i]-1; mi++){
+ #endif
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+   ncom=n;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   pcom=vector(1,n);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   xicom=vector(1,n);
-           }
+   nrfunc=func;
-         for(d=0; d<=dh[mi][i]; d++){
+   for (j=1;j<=n;j++) {
-           newm=savm;
+     pcom[j]=p[j];
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
-           for (kk=1; kk<=cptcovage;kk++) {
+   }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+ #ifdef LINMINORIGINAL
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   xx=1.;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #else
-           savm=oldm;
+   axs=0.0;
-           oldm=newm;
+   xxs=1.;
-         } /* end mult */
+   do{
+     xx= xxs;
-         s1=s[mw[mi][i]][i];
+ #endif
-         s2=s[mw[mi+1][i]][i];
+     ax=0.;
-         bbh=(double)bh[mi][i]/(double)stepm;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
-         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 */
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
-         ipmx +=1;
+     /* 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))   */
-         sw += weight[i];
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
-       } /* end of wave */
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-     } /* end of individual */
+     /* 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]]*/
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+ #ifdef LINMINORIGINAL
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #else
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     if (fx != fx){
-       for(mi=1; mi<= wav[i]-1; mi++){
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+                         printf("|");
-           for (j=1;j<=nlstate+ndeath;j++){
+                         fprintf(ficlog,"|");
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef DEBUGLINMIN
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+                         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
-           }
+ #endif
-         for(d=0; d<dh[mi][i]; d++){
+     }
-           newm=savm;
+   }while(fx != fx && xxs > 1.e-5);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #endif
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef DEBUGLINMIN
-           }
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   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);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #endif
-           savm=oldm;
+ #ifdef LINMINORIGINAL
-           oldm=newm;
+ #else
-         } /* end mult */
+         if(fb == fx){ /* Flat function in the direction */
+                 xmin=xx;
-         s1=s[mw[mi][i]][i];
+     *flat=1;
-         s2=s[mw[mi+1][i]][i];
+         }else{
-         bbh=(double)bh[mi][i]/(double)stepm;
+     *flat=0;
-         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 */
+ #endif
-         ipmx +=1;
+                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
-         sw += weight[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),*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
-       } /* end of wave */
+   /* fmin = f(p[j] + xmin * xi[j]) */
-     } /* end of individual */
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #ifdef DEBUG
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   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(mi=1; mi<= wav[i]-1; mi++){
+   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);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ #endif
-           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);
+                         }
-           }
+ #endif
-         for(d=0; d<dh[mi][i]; d++){
+ #ifdef DEBUGLINMIN
-           newm=savm;
+   printf("linmin end ");
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   fprintf(ficlog,"linmin end ");
-           for (kk=1; kk<=cptcovage;kk++) {
+ #endif
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   for (j=1;j<=n;j++) {
-           }
+ #ifdef LINMINORIGINAL
+     xi[j] *= xmin;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ #else
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef DEBUGLINMIN
-           savm=oldm;
+     if(xxs <1.0)
-           oldm=newm;
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
-         } /* end mult */
+ #endif
+     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
-         s1=s[mw[mi][i]][i];
+ #ifdef DEBUGLINMIN
-         s2=s[mw[mi+1][i]][i];
+     if(xxs <1.0)
-         if( s2 > nlstate){
+       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 );
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ #endif
-         }else{
+ #endif
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-         }
+   }
-         ipmx +=1;
+ #ifdef DEBUGLINMIN
-         sw += weight[i];
+   printf("\n");
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
- /*      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(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-       } /* end of wave */
+   for (j=1;j<=n;j++) {
-     } /* end of individual */
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     if(j % ncovmodel == 0){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       printf("\n");
-       for(mi=1; mi<= wav[i]-1; mi++){
+       fprintf(ficlog,"\n");
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     }
-           for (j=1;j<=nlstate+ndeath;j++){
+   }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #else
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #endif
-           }
+   free_vector(xicom,1,n);
-         for(d=0; d<dh[mi][i]; d++){
+   free_vector(pcom,1,n);
-           newm=savm;
+ }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ /*************** powell ************************/
-           }
+ /*
+ Minimization of a function func of n variables. Input consists of an initial starting point
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-           savm=oldm;
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-           oldm=newm;
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-         } /* end mult */
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
+  */
-         s1=s[mw[mi][i]][i];
+ #ifdef LINMINORIGINAL
-         s2=s[mw[mi+1][i]][i];
+ #else
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         int *flatdir; /* Function is vanishing in that direction */
-         ipmx +=1;
+         int flat=0, flatd=0; /* Function is vanishing in that direction */
-         sw += weight[i];
+ #endif
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         /*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]);*/
+             double (*func)(double []))
-       } /* end of wave */
+ {
-     } /* end of individual */
+ #ifdef LINMINORIGINAL
-   } /* End of if */
+  void linmin(double p[], double xi[], int n, double *fret,
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+               double (*func)(double []));
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ #else
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+  void linmin(double p[], double xi[], int n, double *fret,
-   return -l;
+                                                  double (*func)(double []),int *flat);
- }
+ #endif
+   int i,ibig,j;
- /*************** log-likelihood *************/
+   double del,t,*pt,*ptt,*xit;
- double funcone( double *x)
+   double directest;
- {
+   double fp,fptt;
-   /* Same as likeli but slower because of a lot of printf and if */
+   double *xits;
-   int i, ii, j, k, mi, d, kk;
+   int niterf, itmp;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+ #ifdef LINMINORIGINAL
-   double **out;
+ #else
-   double lli; /* Individual log likelihood */
-   double llt;
+   flatdir=ivector(1,n);
-   int s1, s2;
+   for (j=1;j<=n;j++) flatdir[j]=0;
-   double bbh, survp;
+ #endif
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+   pt=vector(1,n);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   ptt=vector(1,n);
-   /*for(i=1;i<imx;i++)
+   xit=vector(1,n);
-     printf(" %d\n",s[4][i]);
+   xits=vector(1,n);
-   */
+   *fret=(*func)(p);
-   cov[1]=1.;
+   for (j=1;j<=n;j++) pt[j]=p[j];
+   rcurr_time = time(NULL);
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for (*iter=1;;++(*iter)) {
+     fp=(*fret); /* From former iteration or initial value */
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     ibig=0;
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     del=0.0;
-     for(mi=1; mi<= wav[i]-1; mi++){
+     rlast_time=rcurr_time;
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+     /* (void) gettimeofday(&curr_time,&tzp); */
-         for (j=1;j<=nlstate+ndeath;j++){
+     rcurr_time = time(NULL);
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     curr_time = *localtime(&rcurr_time);
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-         }
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-       for(d=0; d<dh[mi][i]; d++){
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-         newm=savm;
+     for (i=1;i<=n;i++) {
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       printf(" %d %.12f",i, p[i]);
-         for (kk=1; kk<=cptcovage;kk++) {
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       fprintf(ficrespow," %.12lf", p[i]);
-         }
+     }
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     printf("\n");
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     fprintf(ficlog,"\n");
-         savm=oldm;
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-         oldm=newm;
+     if(*iter <=3){
-       } /* end mult */
+       tml = *localtime(&rcurr_time);
+       strcpy(strcurr,asctime(&tml));
-       s1=s[mw[mi][i]][i];
+       rforecast_time=rcurr_time;
-       s2=s[mw[mi+1][i]][i];
+       itmp = strlen(strcurr);
-       bbh=(double)bh[mi][i]/(double)stepm;
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       /* bias is positive if real duration
+                                 strcurr[itmp-1]='\0';
-        * is higher than the multiple of stepm and negative otherwise.
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-        */
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+       for(niterf=10;niterf<=30;niterf+=10){
-         lli=log(out[s1][s2] - savm[s1][s2]);
+                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-       } else if  (s2==-2) {
+                                 forecast_time = *localtime(&rforecast_time);
-         for (j=1,survp=0. ; j<=nlstate; j++)
+                                 strcpy(strfor,asctime(&forecast_time));
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+                                 itmp = strlen(strfor);
-         lli= log(survp);
+                                 if(strfor[itmp-1]=='\n')
-       }else if (mle==1){
+                                         strfor[itmp-1]='\0';
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+                                 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);
-       } else if(mle==2){
+                                 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);
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       }
-       } else if(mle==3){  /* exponential inter-extrapolation */
+     }
-         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+     for (i=1;i<=n;i++) { /* For each direction i */
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-         lli=log(out[s1][s2]); /* Original formula */
+       fptt=(*fret);
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+ #ifdef DEBUG
-         lli=log(out[s1][s2]); /* Original formula */
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       } /* End of if */
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       ipmx +=1;
+ #endif
-       sw += weight[i];
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       fprintf(ficlog,"%d",i);fflush(ficlog);
- /*       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 LINMINORIGINAL
-       if(globpr){
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+ #else
-  %11.6f %11.6f %11.6f ", \
+       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+                         flatdir[i]=flat; /* Function is vanishing in that direction i */
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+ #endif
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+                         /* Outputs are fret(new point p) p is updated and xit rescaled */
-           llt +=ll[k]*gipmx/gsw;
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+                                 /* because that direction will be replaced unless the gain del is small */
-         }
+                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-         fprintf(ficresilk," %10.6f\n", -llt);
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-       }
+                                 /* with the new direction. */
-     } /* end of wave */
+                                 del=fabs(fptt-(*fret));
-   } /* end of individual */
+                                 ibig=i;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+       }
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ #ifdef DEBUG
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+       printf("%d %.12e",i,(*fret));
-   if(globpr==0){ /* First time we count the contributions and weights */
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-     gipmx=ipmx;
+       for (j=1;j<=n;j++) {
-     gsw=sw;
+                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-   }
+                                 printf(" x(%d)=%.12e",j,xit[j]);
-   return -l;
+                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
- }
+       }
+       for(j=1;j<=n;j++) {
+                                 printf(" p(%d)=%.12e",j,p[j]);
- /*************** function likelione ***********/
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+       }
- {
+       printf("\n");
-   /* This routine should help understanding what is done with
+       fprintf(ficlog,"\n");
-      the selection of individuals/waves and
+ #endif
-      to check the exact contribution to the likelihood.
+     } /* end loop on each direction i */
-      Plotting could be done.
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-    */
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-   int k;
+     /* New value of last point Pn is not computed, P(n-1) */
+       for(j=1;j<=n;j++) {
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+                                 if(flatdir[j] >0){
-     strcpy(fileresilk,"ilk");
+                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-     strcat(fileresilk,fileres);
+                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+                                 }
-       printf("Problem with resultfile: %s\n", fileresilk);
+                                 /* printf("\n"); */
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+                                 /* 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");
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
-     for(k=1; k<=nlstate; k++)
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+       /* decreased of more than 3.84  */
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
-   }
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
+       /* By adding 10 parameters more the gain should be 18.31 */
-   *fretone=(*funcone)(p);
-   if(*globpri !=0){
+       /* Starting the program with initial values given by a former maximization will simply change */
-     fclose(ficresilk);
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
-     fflush(fichtm);
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
-   }
+ #ifdef DEBUG
-   return;
+       int k[2],l;
- }
+       k[0]=1;
+       k[1]=-1;
+       printf("Max: %.12e",(*func)(p));
- /*********** Maximum Likelihood Estimation ***************/
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         printf(" %.12e",p[j]);
- {
+         fprintf(ficlog," %.12e",p[j]);
-   int i,j, iter;
+       }
-   double **xi;
+       printf("\n");
-   double fret;
+       fprintf(ficlog,"\n");
-   double fretone; /* Only one call to likelihood */
+       for(l=0;l<=1;l++) {
-   /*  char filerespow[FILENAMELENGTH];*/
+         for (j=1;j<=n;j++) {
-   xi=matrix(1,npar,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++)
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         }
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   strcpy(filerespow,"pow");
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   strcat(filerespow,fileres);
+       }
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ #endif
-     printf("Problem with resultfile: %s\n", filerespow);
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ #ifdef LINMINORIGINAL
-   }
+ #else
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+       free_ivector(flatdir,1,n);
-   for (i=1;i<=nlstate;i++)
+ #endif
-     for(j=1;j<=nlstate+ndeath;j++)
+       free_vector(xit,1,n);
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       free_vector(xits,1,n);
-   fprintf(ficrespow,"\n");
+       free_vector(ptt,1,n);
+       free_vector(pt,1,n);
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+       return;
+     } /* enough precision */
-   free_matrix(xi,1,npar,1,npar);
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-   fclose(ficrespow);
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+       ptt[j]=2.0*p[j]-pt[j];
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       xit[j]=p[j]-pt[j];
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       pt[j]=p[j];
+     }
- }
+     fptt=(*func)(ptt); /* f_3 */
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
- /**** Computes Hessian and covariance matrix ***/
+                 if (*iter <=4) {
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ #else
- {
+ #endif
-   double  **a,**y,*x,pd;
+ #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
-   double **hess;
+ #else
-   int i, j,jk;
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-   int *indx;
+ #endif
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-   double gompertz(double p[]);
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
-   hess=matrix(1,npar,1,npar);
+       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
+       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+       /*  Even if f3 <f1, directest can be negative and t >0 */
-   for (i=1;i<=npar;i++){
+       /* mu² and del² are equal when f3=f1 */
-     printf("%d",i);fflush(stdout);
+                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
+                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
+ #ifdef NRCORIGINAL
-     /*  printf(" %f ",p[i]);
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+ #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);
-   for (i=1;i<=npar;i++) {
+ #endif
-     for (j=1;j<=npar;j++)  {
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
-       if (j>i) {
+ #ifdef DEBUG
-         printf(".%d%d",i,j);fflush(stdout);
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+       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);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-         hess[j][i]=hess[i][j];
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-         /*printf(" %lf ",hess[i][j]);*/
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       }
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-     }
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-   }
+ #endif
-   printf("\n");
+ #ifdef POWELLORIGINAL
-   fprintf(ficlog,"\n");
+       if (t < 0.0) { /* Then we use it for new direction */
+ #else
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+                                 printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-   a=matrix(1,npar,1,npar);
+         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);
-   y=matrix(1,npar,1,npar);
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-   x=vector(1,npar);
+       }
-   indx=ivector(1,npar);
+       if (directest < 0.0) { /* Then we use it for new direction */
-   for (i=1;i<=npar;i++)
+ #endif
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+ #ifdef DEBUGLINMIN
-   ludcmp(a,npar,indx,&pd);
+                                 printf("Before linmin in direction P%d-P0\n",n);
+                                 for (j=1;j<=n;j++) {
-   for (j=1;j<=npar;j++) {
+                                         printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-     for (i=1;i<=npar;i++) x[i]=0;
+                                         fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-     x[j]=1;
+                                         if(j % ncovmodel == 0){
-     lubksb(a,npar,indx,x);
+                                                 printf("\n");
-     for (i=1;i<=npar;i++){
+                                                 fprintf(ficlog,"\n");
-       matcov[i][j]=x[i];
+                                         }
-     }
+                                 }
-   }
+ #endif
+ #ifdef LINMINORIGINAL
-   printf("\n#Hessian matrix#\n");
+                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+ #else
-   for (i=1;i<=npar;i++) {
+                                 linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-     for (j=1;j<=npar;j++) {
+                                 flatdir[i]=flat; /* Function is vanishing in that direction i */
-       printf("%.3e ",hess[i][j]);
+ #endif
-       fprintf(ficlog,"%.3e ",hess[i][j]);
-     }
+ #ifdef DEBUGLINMIN
-     printf("\n");
+                                 for (j=1;j<=n;j++) {
-     fprintf(ficlog,"\n");
+                                         printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-   }
+                                         fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+                                         if(j % ncovmodel == 0){
-   /* Recompute Inverse */
+                                                 printf("\n");
-   for (i=1;i<=npar;i++)
+                                                 fprintf(ficlog,"\n");
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+                                         }
-   ludcmp(a,npar,indx,&pd);
+                                 }
+ #endif
-   /*  printf("\n#Hessian matrix recomputed#\n");
+                                 for (j=1;j<=n;j++) {
+                                         xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-   for (j=1;j<=npar;j++) {
+                                         xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-     for (i=1;i<=npar;i++) x[i]=0;
+                                 }
-     x[j]=1;
+ #ifdef LINMINORIGINAL
-     lubksb(a,npar,indx,x);
+ #else
-     for (i=1;i<=npar;i++){
+                                 for (j=1, flatd=0;j<=n;j++) {
-       y[i][j]=x[i];
+                                         if(flatdir[j]>0)
-       printf("%.3e ",y[i][j]);
+                                                 flatd++;
-       fprintf(ficlog,"%.3e ",y[i][j]);
+                                 }
-     }
+                                 if(flatd >0){
-     printf("\n");
+                                         printf("%d flat directions\n",flatd);
-     fprintf(ficlog,"\n");
+                                         fprintf(ficlog,"%d flat directions\n",flatd);
-   }
+                                         for (j=1;j<=n;j++) {
-   */
+                                                 if(flatdir[j]>0){
+                                                         printf("%d ",j);
-   free_matrix(a,1,npar,1,npar);
+                                                         fprintf(ficlog,"%d ",j);
-   free_matrix(y,1,npar,1,npar);
+                                                 }
-   free_vector(x,1,npar);
+                                         }
-   free_ivector(indx,1,npar);
+                                         printf("\n");
-   free_matrix(hess,1,npar,1,npar);
+                                         fprintf(ficlog,"\n");
+                                 }
+ #endif
- }
+                                 printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+                                 fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
- /*************** hessian matrix ****************/
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+ #ifdef DEBUG
- {
+                                 printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   int i;
+                                 fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   int l=1, lmax=20;
+                                 for(j=1;j<=n;j++){
-   double k1,k2;
+                                         printf(" %lf",xit[j]);
-   double p2[NPARMAX+1];
+                                         fprintf(ficlog," %lf",xit[j]);
-   double res;
+                                 }
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+                                 printf("\n");
-   double fx;
+                                 fprintf(ficlog,"\n");
-   int k=0,kmax=10;
+ #endif
-   double l1;
+       } /* end of t or directest negative */
+ #ifdef POWELLNOF3INFF1TEST
-   fx=func(x);
+ #else
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+     } /* end if (fptt < fp)  */
-   for(l=0 ; l <=lmax; l++){
+ #endif
-     l1=pow(10,l);
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-     delts=delt;
+                 } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
-     for(k=1 ; k <kmax; k=k+1){
+ #else
-       delt = delta*(l1*k);
+ #endif
-       p2[theta]=x[theta] +delt;
+   } /* loop iteration */
-       k1=func(p2)-fx;
+ }
-       p2[theta]=x[theta]-delt;
-       k2=func(p2)-fx;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
+ {
- #ifdef DEBUG
+   /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
-       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);
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-       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);
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
- #endif
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-         k=kmax;
+   /* Initial matrix pimij */
-       }
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-         k=kmax; l=lmax*10.;
+   /*  0,                   0                  , 1} */
-       }
+   /*
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+    * and after some iteration: */
-         delts=delt;
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-       }
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-     }
+   /*  0,                   0                  , 1} */
-   }
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-   delti[theta]=delts;
+   /* {0.51571254859325999, 0.4842874514067399, */
-   return res;
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
- }
+   int i, ii,j,k;
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
- {
+   /* double **matprod2(); */ /* test */
-   int i;
+   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
-   int l=1, l1, lmax=20;
+   double **newm;
-   double k1,k2,k3,k4,res,fx;
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-   double p2[NPARMAX+1];
+   int ncvloop=0;
-   int k;
+   min=vector(1,nlstate);
-   fx=func(x);
+   max=vector(1,nlstate);
-   for (k=1; k<=2; k++) {
+   meandiff=vector(1,nlstate);
-     for (i=1;i<=npar;i++) p2[i]=x[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         /* Starting with matrix unity */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-     k1=func(p2)-fx;
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     }
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     k2=func(p2)-fx;
+   cov[1]=1.;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-     k3=func(p2)-fx;
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     ncvloop++;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     newm=savm;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     /* Covariates have to be included here again */
-     k4=func(p2)-fx;
+     cov[2]=agefin;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     if(nagesqr==1)
- #ifdef DEBUG
+       cov[3]= agefin*agefin;;
-     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 (k=1; k<=cptcovn;k++) {
-     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);
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
- #endif
+                         /* Here comes the value of the covariate 'ij' */
-   }
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-   return res;
+       /* 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])]); */
- }
+     }
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
- /************** Inverse of matrix **************/
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
- void ludcmp(double **a, int n, int *indx, double *d)
+     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 */
-   int i,imax,j,k;
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-   double big,dum,sum,temp;
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-   double *vv;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-   vv=vector(1,n);
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-   *d=1.0;
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-   for (i=1;i<=n;i++) {
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-     big=0.0;
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-     for (j=1;j<=n;j++)
+                 /* age and covariate values of ij are in 'cov' */
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     vv[i]=1.0/big;
+     savm=oldm;
-   }
+     oldm=newm;
-   for (j=1;j<=n;j++) {
-     for (i=1;i<j;i++) {
+     for(j=1; j<=nlstate; j++){
-       sum=a[i][j];
+       max[j]=0.;
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+       min[j]=1.;
-       a[i][j]=sum;
+     }
-     }
+     for(i=1;i<=nlstate;i++){
-     big=0.0;
+       sumnew=0;
-     for (i=j;i<=n;i++) {
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-       sum=a[i][j];
+       for(j=1; j<=nlstate; j++){
-       for (k=1;k<j;k++)
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-         sum -= a[i][k]*a[k][j];
+         max[j]=FMAX(max[j],prlim[i][j]);
-       a[i][j]=sum;
+         min[j]=FMIN(min[j],prlim[i][j]);
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+       }
-         big=dum;
+     }
-         imax=i;
-       }
+     maxmax=0.;
-     }
+     for(j=1; j<=nlstate; j++){
-     if (j != imax) {
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
-       for (k=1;k<=n;k++) {
+       maxmax=FMAX(maxmax,meandiff[j]);
-         dum=a[imax][k];
+       /* 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); */
-         a[imax][k]=a[j][k];
+     } /* j loop */
-         a[j][k]=dum;
+     *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); */
-       *d = -(*d);
+     if(maxmax < ftolpl){
-       vv[imax]=vv[j];
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-     }
+       free_vector(min,1,nlstate);
-     indx[j]=imax;
+       free_vector(max,1,nlstate);
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+       free_vector(meandiff,1,nlstate);
-     if (j != n) {
+       return prlim;
-       dum=1.0/(a[j][j]);
+     }
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   } /* age loop */
-     }
+     /* After some age loop it doesn't converge */
-   }
+   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
-   free_vector(vv,1,n);  /* Doesn't work */
+ Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
- ;
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
- }
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
- void lubksb(double **a, int n, int *indx, double b[])
+   free_vector(meandiff,1,nlstate);
- {
-   int i,ii=0,ip,j;
+   return prlim; /* should not reach here */
-   double sum;
+ }
-   for (i=1;i<=n;i++) {
-     ip=indx[i];
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
-     sum=b[ip];
-     b[ip]=b[i];
+  /* 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) */
-     if (ii)
+  /* 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) */
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
-     else if (sum) ii=i;
+ {
-     b[i]=sum;
+   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
-   }
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-   for (i=n;i>=1;i--) {
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-     sum=b[i];
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-     b[i]=sum/a[i][i];
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-   }
+   /* Initial matrix pimij */
- }
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
- void pstamp(FILE *fichier)
+   /*  0,                   0                  , 1} */
- {
+   /*
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+    * and after some iteration: */
- }
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
- /************ Frequencies ********************/
+   /*  0,                   0                  , 1} */
- 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[])
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
- {  /* Some frequencies */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   /* If we start from prlim again, prlim tends to a constant matrix */
-   int first;
-   double ***freq; /* Frequencies */
+   int i, ii,j,k;
-   double *pp, **prop;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   /* double **matprod2(); */ /* test */
-   char fileresp[FILENAMELENGTH];
+   double **out, cov[NCOVMAX+1], **bmij();
+   double **newm;
-   pp=vector(1,nlstate);
+   double         **dnewm, **doldm, **dsavm;  /* for use */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   double         **oldm, **savm;  /* for use */
-   strcpy(fileresp,"p");
-   strcat(fileresp,fileres);
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   int ncvloop=0;
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   min=vector(1,nlstate);
-     exit(0);
+   max=vector(1,nlstate);
-   }
+   meandiff=vector(1,nlstate);
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-   j1=0;
+         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+         oldm=oldms; savm=savms;
-   j=cptcoveff;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         /* Starting with matrix unity */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   first=1;
+                 for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   for(k1=1; k1<=j;k1++){
+     }
-     for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
+   cov[1]=1.;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         scanf("%d", i);*/
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       for (i=-5; i<=nlstate+ndeath; i++)
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-           for(m=iagemin; m <= iagemax+3; m++)
+   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
-             freq[i][jk][m]=0;
+     ncvloop++;
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
-     for (i=1; i<=nlstate; i++)
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
-       for(m=iagemin; m <= iagemax+3; m++)
+     /* Covariates have to be included here again */
-         prop[i][m]=0;
+     cov[2]=agefin;
+     if(nagesqr==1)
-       dateintsum=0;
+       cov[3]= agefin*agefin;;
-       k2cpt=0;
+     for (k=1; k<=cptcovn;k++) {
-       for (i=1; i<=imx; i++) {
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-         bool=1;
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-         if  (cptcovn>0) {
+       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
-           for (z1=1; z1<=cptcoveff; z1++)
+     }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-               bool=0;
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-         }
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
-         if (bool==1){
+     for (k=1; k<=cptcovprod;k++) /* Useless */
-           for(m=firstpass; m<=lastpass; m++){
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-             k2=anint[m][i]+(mint[m][i]/12.);
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-               if (m<lastpass) {
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+                 /* ij should be linked to the correct index of cov */
-               }
+                 /* age and covariate values ij are in 'cov', but we need to pass
+                  * ij for the observed prevalence at age and status and covariate
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+                  * number:  prevacurrent[(int)agefin][ii][ij]
-                 dateintsum=dateintsum+k2;
+                  */
-                 k2cpt++;
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
-               }
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
-               /*}*/
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
-           }
+     savm=oldm;
-         }
+     oldm=newm;
-       }
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       min[j]=1.;
-       pstamp(ficresp);
+     }
-       if  (cptcovn>0) {
+     for(j=1; j<=nlstate; j++){
-         fprintf(ficresp, "\n#********** Variable ");
+       for(i=1;i<=nlstate;i++){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
-         fprintf(ficresp, "**********\n#");
+                                 bprlim[i][j]= newm[i][j];
-       }
+                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
-       for(i=1; i<=nlstate;i++)
+                                 min[i]=FMIN(min[i],bprlim[i][j]);
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       }
-       fprintf(ficresp, "\n");
+     }
-       for(i=iagemin; i <= iagemax+3; i++){
+     maxmax=0.;
-         if(i==iagemax+3){
+     for(i=1; i<=nlstate; i++){
-           fprintf(ficlog,"Total");
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
-         }else{
+       maxmax=FMAX(maxmax,meandiff[i]);
-           if(first==1){
+       /* 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); */
-             first=0;
+     } /* j loop */
-             printf("See log file for details...\n");
+     *ncvyear= -( (int)age- (int)agefin);
-           }
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
-           fprintf(ficlog,"Age %d", i);
+     if(maxmax < ftolpl){
-         }
+       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-         for(jk=1; jk <=nlstate ; jk++){
+       free_vector(min,1,nlstate);
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       free_vector(max,1,nlstate);
-             pp[jk] += freq[jk][m][i];
+       free_vector(meandiff,1,nlstate);
-         }
+       return bprlim;
-         for(jk=1; jk <=nlstate ; jk++){
+     }
-           for(m=-1, pos=0; m <=0 ; m++)
+   } /* age loop */
-             pos += freq[jk][m][i];
+     /* After some age loop it doesn't converge */
-           if(pp[jk]>=1.e-10){
+   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'. \n\
-             if(first==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);
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   /* 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);
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   free_vector(max,1,nlstate);
-           }else{
+   free_vector(meandiff,1,nlstate);
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   return bprlim; /* should not reach here */
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+ }
-           }
-         }
+ /*************** transition probabilities ***************/
-         for(jk=1; jk <=nlstate ; jk++){
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+ {
-             pp[jk] += freq[jk][m][i];
+   /* 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
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+      model to the ncovmodel covariates (including constant and age).
-           pos += pp[jk];
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-           posprop += prop[jk][i];
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         }
+      ncth covariate in the global vector x is given by the formula:
-         for(jk=1; jk <=nlstate ; jk++){
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-           if(pos>=1.e-5){
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-             if(first==1)
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-           }else{
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-             if(first==1)
+   */
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double s1, lnpijopii;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   /*double t34;*/
-           }
+   int i,j, nc, ii, jj;
-           if( i <= iagemax){
-             if(pos>=1.e-5){
+   for(i=1; i<= nlstate; i++){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+     for(j=1; j<i;j++){
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-             }
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-             else
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+       }
-           }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         }
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+     }
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+     for(j=i+1; j<=nlstate+ndeath;j++){
-           for(m=-1; m <=nlstate+ndeath; m++)
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-             if(freq[jk][m][i] !=0 ) {
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-             if(first==1)
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+       }
-             }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         if(i <= iagemax)
+     }
-           fprintf(ficresp,"\n");
+   }
-         if(first==1)
-           printf("Others in log...\n");
+   for(i=1; i<= nlstate; i++){
-         fprintf(ficlog,"\n");
+     s1=0;
-       }
+     for(j=1; j<i; j++){
-     }
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   }
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   dateintmean=dateintsum/k2cpt;
+     }
+     for(j=i+1; j<=nlstate+ndeath; j++){
-   fclose(ficresp);
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   free_vector(pp,1,nlstate);
+     }
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-   /* End of Freq */
+     ps[i][i]=1./(s1+1.);
- }
+     /* Computing other pijs */
+     for(j=1; j<i; j++)
- /************ Prevalence ********************/
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
- 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(j=i+1; j<=nlstate+ndeath; j++)
- {
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+   } /* end i */
-      We still use firstpass and lastpass as another selection.
-   */
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+       ps[ii][jj]=0;
-   double ***freq; /* Frequencies */
+       ps[ii][ii]=1;
-   double *pp, **prop;
+     }
-   double pos,posprop;
+   }
-   double  y2; /* in fractional years */
-   int iagemin, iagemax;
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-   iagemin= (int) agemin;
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-   iagemax= (int) agemax;
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-   /*pp=vector(1,nlstate);*/
+   /*   } */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   /*   printf("\n "); */
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+   /* } */
-   j1=0;
+   /* printf("\n ");printf("%lf ",cov[2]);*/
+   /*
-   j=cptcoveff;
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+                 goto end;*/
+   return ps;
-   for(k1=1; k1<=j;k1++){
+ }
-     for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
+ /*************** backward transition probabilities ***************/
-       for (i=1; i<=nlstate; i++)
+  /* 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 ) */
-         for(m=iagemin; m <= iagemax+3; m++)
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-           prop[i][m]=0.0;
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
+ {
-       for (i=1; i<=imx; i++) { /* Each individual */
+   /* Computes the backward probability at age agefin and covariate ij
-         bool=1;
+    * and returns in **ps as well as **bmij.
-         if  (cptcovn>0) {
+    */
-           for (z1=1; z1<=cptcoveff; z1++)
+   int i, ii, j,k;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+   double **out, **pmij();
-         }
+   double sumnew=0.;
-         if (bool==1) {
+   double agefin;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+   double **dnewm, **dsavm, **doldm;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+   double **bbmij;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   doldm=ddoldms; /* global pointers */
-               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);
+   dnewm=ddnewms;
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+   dsavm=ddsavms;
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   agefin=cov[2];
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
-               }
+      the observed prevalence (with this covariate ij) */
-             }
+   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
-           } /* end selection of waves */
+   /* We do have the matrix Px in savm  and we need pij */
-         }
+   for (j=1;j<=nlstate+ndeath;j++){
-       }
+     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
-       for(i=iagemin; i <= iagemax+3; i++){
+     for (ii=1;ii<=nlstate;ii++){
+       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
-           posprop += prop[jk][i];
+     for (ii=1;ii<=nlstate+ndeath;ii++){
-         }
+       if(sumnew >= 1.e-10){
+         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
-         for(jk=1; jk <=nlstate ; jk++){
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
-           if( i <=  iagemax){
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
-             if(posprop>=1.e-5){
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+         /* }else */
-             }
+         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
-           }
+       }else{
-         }/* end jk */
+         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
-       }/* end i */
+       }
-     } /* end i1 */
+     } /*End ii */
-   } /* end k1 */
+   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
+   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
-   /*free_vector(pp,1,nlstate);*/
+   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
- }  /* End of prevalence */
+   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
+   /* left Product of this matrix by diag matrix of prevalences (savm) */
- /************* Waves Concatenation ***************/
+   for (j=1;j<=nlstate+ndeath;j++){
+     for (ii=1;ii<=nlstate+ndeath;ii++){
- 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)
+       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
- {
+     }
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
-      Death is a valid wave (if date is known).
+   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+   /* end bmij */
-      and mw[mi+1][i]. dh depends on stepm.
+   return ps;
-      */
+ }
+ /*************** transition probabilities ***************/
-   int i, mi, m;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+ double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-      double sum=0., jmean=0.;*/
+ {
-   int first;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-   int j, k=0,jk, ju, jl;
+      computes the probability to be observed in state j being in state i by appying the
-   double sum=0.;
+      model to the ncovmodel covariates (including constant and age).
-   first=0;
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-   jmin=1e+5;
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-   jmax=-1;
+      ncth covariate in the global vector x is given by the formula:
-   jmean=0.;
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-   for(i=1; i<=imx; i++){
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-     mi=0;
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-     m=firstpass;
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-     while(s[m][i] <= nlstate){
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         mw[++mi][i]=m;
+   */
-       if(m >=lastpass)
+   double s1, lnpijopii;
-         break;
+   /*double t34;*/
-       else
+   int i,j, nc, ii, jj;
-         m++;
-     }/* end while */
+         for(i=1; i<= nlstate; i++){
-     if (s[m][i] > nlstate){
+                 for(j=1; j<i;j++){
-       mi++;     /* Death is another wave */
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-       /* if(mi==0)  never been interviewed correctly before death */
+                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
-          /* Only death is a correct wave */
+                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-       mw[mi][i]=m;
+                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     }
+                         }
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-     wav[i]=mi;
+                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     if(mi==0){
+                 }
-       nbwarn++;
+                 for(j=i+1; j<=nlstate+ndeath;j++){
-       if(first==0){
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-         first=1;
+                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-       }
+                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-       if(first==1){
+                         }
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       }
+                 }
-     } /* end mi==0 */
+         }
-   } /* End individuals */
+         for(i=1; i<= nlstate; i++){
-   for(i=1; i<=imx; i++){
+                 s1=0;
-     for(mi=1; mi<wav[i];mi++){
+                 for(j=1; j<i; j++){
-       if (stepm <=0)
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         dh[mi][i]=1;
+                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       else{
+                 }
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+                 for(j=i+1; j<=nlstate+ndeath; j++){
-           if (agedc[i] < 2*AGESUP) {
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-             if(j==0) j=1;  /* Survives at least one month after exam */
+                 }
-             else if(j<0){
+                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-               nberr++;
+                 ps[i][i]=1./(s1+1.);
-               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]);
+                 /* Computing other pijs */
-               j=1; /* Temporary Dangerous patch */
+                 for(j=1; j<i; j++)
-               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);
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+                 for(j=i+1; j<=nlstate+ndeath; j++)
-               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);
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-             }
+                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-             k=k+1;
+         } /* end i */
-             if (j >= jmax){
-               jmax=j;
+         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-               ijmax=i;
+                 for(jj=1; jj<= nlstate+ndeath; jj++){
-             }
+                         ps[ii][jj]=0;
-             if (j <= jmin){
+                         ps[ii][ii]=1;
-               jmin=j;
+                 }
-               ijmin=i;
+         }
-             }
+         /* Added for backcast */ /* Transposed matrix too */
-             sum=sum+j;
+         for(jj=1; jj<= nlstate+ndeath; jj++){
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+                 s1=0.;
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+                 for(ii=1; ii<= nlstate+ndeath; ii++){
-           }
+                         s1+=ps[ii][jj];
-         }
+                 }
-         else{
+                 for(ii=1; ii<= nlstate; ii++){
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+                         ps[ii][jj]=ps[ii][jj]/s1;
- /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+                 }
+         }
-           k=k+1;
+         /* Transposition */
-           if (j >= jmax) {
+         for(jj=1; jj<= nlstate+ndeath; jj++){
-             jmax=j;
+                 for(ii=jj; ii<= nlstate+ndeath; ii++){
-             ijmax=i;
+                         s1=ps[ii][jj];
-           }
+                         ps[ii][jj]=ps[jj][ii];
-           else if (j <= jmin){
+                         ps[jj][ii]=s1;
-             jmin=j;
+                 }
-             ijmin=i;
+         }
-           }
+         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-           /*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]);*/
+         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-           if(j<0){
+         /*   } */
-             nberr++;
+         /*   printf("\n "); */
-             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]);
+         /* printf("\n ");printf("%lf ",cov[2]);*/
-           }
+         /*
-           sum=sum+j;
+                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
-         }
+                 goto end;*/
-         jk= j/stepm;
+         return ps;
-         jl= j -jk*stepm;
+ }
-         ju= j -(jk+1)*stepm;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           if(jl==0){
+ /**************** Product of 2 matrices ******************/
-             dh[mi][i]=jk;
-             bh[mi][i]=0;
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-           }else{ /* We want a negative bias in order to only have interpolation ie
+ {
-                   * at the price of an extra matrix product in likelihood */
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-             dh[mi][i]=jk+1;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-             bh[mi][i]=ju;
+   /* in, b, out are matrice of pointers which should have been initialized
-           }
+      before: only the contents of out is modified. The function returns
-         }else{
+      a pointer to pointers identical to out */
-           if(jl <= -ju){
+   int i, j, k;
-             dh[mi][i]=jk;
+   for(i=nrl; i<= nrh; i++)
-             bh[mi][i]=jl;       /* bias is positive if real duration
+     for(k=ncolol; k<=ncoloh; k++){
-                                  * is higher than the multiple of stepm and negative otherwise.
+       out[i][k]=0.;
-                                  */
+       for(j=ncl; j<=nch; j++)
-           }
+         out[i][k] +=in[i][j]*b[j][k];
-           else{
+     }
-             dh[mi][i]=jk+1;
+   return out;
-             bh[mi][i]=ju;
+ }
-           }
-           if(dh[mi][i]==0){
-             dh[mi][i]=1; /* At least one step */
+ /************* Higher Matrix Product ***************/
-             bh[mi][i]=ju; /* At least one step */
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-           }
+ {
-         } /* end if mle */
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
-       }
+      'nhstepm*hstepm*stepm' months (i.e. until
-     } /* end wave */
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   }
+      nhstepm*hstepm matrices.
-   jmean=sum/k;
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   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);
+      (typically every 2 years instead of every month which is too big
-   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);
+      for the memory).
-  }
+      Model is determined by parameters x and covariates have to be
+      included manually here.
- /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx)
+      */
- {
+   int i, j, d, h, k;
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   double **out, cov[NCOVMAX+1];
-   int cptcode=0;
+   double **newm;
-   cptcoveff=0;
+   double agexact;
+   double agebegin, ageend;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+     for (j=1;j<=nlstate+ndeath;j++){
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-                                modality*/
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+     }
-       Ndum[ij]++; /*store the modality */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+   for(h=1; h <=nhstepm; h++){
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+     for(d=1; d <=hstepm; d++){
-                                        Tvar[j]. If V=sex and male is 0 and
+       newm=savm;
-                                        female is 1, then  cptcode=1.*/
+       /* Covariates have to be included here again */
-     }
+       cov[1]=1.;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-     for (i=0; i<=cptcode; i++) {
+       cov[2]=agexact;
-       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 */
+       if(nagesqr==1)
-     }
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++)
-     ij=1;
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-     for (i=1; i<=ncodemax[j]; i++) {
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-       for (k=0; k<= maxncov; k++) {
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-         if (Ndum[k] != 0) {
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           nbcode[Tvar[j]][ij]=k;
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-           /* 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; */
+       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-           ij++;
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-         }
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-         if (ij > ncodemax[j]) break;
-       }
-     }
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-   }
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+                         /* right multiplication of oldm by the current matrix */
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-  for (i=1; i<=ncovmodel-2; i++) {
+       /* if((int)age == 70){ */
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
-    ij=Tvar[i];
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
-    Ndum[ij]++;
+       /*          printf("%d pmmij ",i); */
-  }
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
-  ij=1;
+       /*          } */
-  for (i=1; i<= maxncov; i++) {
+       /*          printf(" oldm "); */
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-      Tvaraff[ij]=i; /*For printing */
+       /*            printf("%f ",oldm[i][j]); */
-      ij++;
+       /*          } */
-    }
+       /*          printf("\n"); */
-  }
+       /*        } */
+       /* } */
-  cptcoveff=ij-1; /*Number of simple covariates*/
+       savm=oldm;
- }
+       oldm=newm;
+     }
- /*********** Health Expectancies ****************/
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
- 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[] )
+                                 po[i][j][h]=newm[i][j];
+                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
- {
+       }
-   /* Health expectancies, no variances */
+     /*printf("h=%d ",h);*/
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   } /* end h */
-   double age, agelim, hf;
+         /*     printf("\n H=%d \n",h); */
-   double ***p3mat;
+   return po;
-   double eip;
+ }
-   pstamp(ficreseij);
+ /************* Higher Back Matrix Product ***************/
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+ /* 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 ) */
-   fprintf(ficreseij,"# Age");
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
-   for(i=1; i<=nlstate;i++){
+ {
-     for(j=1; j<=nlstate;j++){
+   /* Computes the transition matrix starting at age 'age' over
-       fprintf(ficreseij," e%1d%1d ",i,j);
+      'nhstepm*hstepm*stepm' months (i.e. until
-     }
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-     fprintf(ficreseij," e%1d. ",i);
+      nhstepm*hstepm matrices.
-   }
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   fprintf(ficreseij,"\n");
+      (typically every 2 years instead of every month which is too big
+      for the memory).
+      Model is determined by parameters x and covariates have to be
-   if(estepm < stepm){
+      included manually here.
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+   */
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   int i, j, d, h, k;
-    * This is mainly to measure the difference between two models: for example
+   double **out, cov[NCOVMAX+1];
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   double **newm;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   double agexact;
-    * progression in between and thus overestimating or underestimating according
+   double agebegin, ageend;
-    * to the curvature of the survival function. If, for the same date, we
+   double **oldm, **savm;
-    * 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
+   oldm=oldms;savm=savms;
-    * hypothesis. A more precise result, taking into account a more precise
+   /* Hstepm could be zero and should return the unit matrix */
-    * curvature will be obtained if estepm is as small as stepm. */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
-   /* For example we decided to compute the life expectancy with the smallest unit */
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-      nhstepm is the number of hstepm from age to agelim
+     }
-      nstepm is the number of stepm from age to agelin.
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-      Look at hpijx to understand the reason of that which relies in memory size
+   for(h=1; h <=nhstepm; h++){
-      and note for a fixed period like estepm months */
+     for(d=1; d <=hstepm; d++){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       newm=savm;
-      survival function given by stepm (the optimization length). Unfortunately it
+       /* Covariates have to be included here again */
-      means that if the survival funtion is printed only each two years of age and if
+       cov[1]=1.;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-      results. So we changed our mind and took the option of the best precision.
+       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
-   */
+       cov[2]=agexact;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       if(nagesqr==1)
+         cov[3]= agexact*agexact;
-   agelim=AGESUP;
+       for (k=1; k<=cptcovn;k++)
-   /* If stepm=6 months */
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
- /* nhstepm age range expressed in number of stepm */
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-   /* if (stepm >= YEARM) hstepm=1;*/
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   for (age=bage; age<=fage; age ++){
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       /* Careful transposed matrix */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       /* age is in cov[2] */
+       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
-     printf("%d|",(int)age);fflush(stdout);
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+       /* if((int)age == 70){ */
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
-     /* Computing expectancies */
+       /*          printf("%d pmmij ",i); */
-     for(i=1; i<=nlstate;i++)
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-       for(j=1; j<=nlstate;j++)
+       /*            printf("%f ",pmmij[i][j]); */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+       /*          } */
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-           /*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]);*/
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
-         }
+       /*          printf("\n"); */
+       /*        } */
-     fprintf(ficreseij,"%3.0f",age );
+       /* } */
-     for(i=1; i<=nlstate;i++){
+       savm=oldm;
-       eip=0;
+       oldm=newm;
-       for(j=1; j<=nlstate;j++){
+     }
-         eip +=eij[i][j][(int)age];
+     for(i=1; i<=nlstate+ndeath; i++)
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       for(j=1;j<=nlstate+ndeath;j++) {
-       }
+         po[i][j][h]=newm[i][j];
-       fprintf(ficreseij,"%9.4f", eip );
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-     }
+       }
-     fprintf(ficreseij,"\n");
+     /*printf("h=%d ",h);*/
+   } /* end h */
-   }
+   /*     printf("\n H=%d \n",h); */
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   return po;
-   printf("\n");
+ }
-   fprintf(ficlog,"\n");
- }
+ #ifdef NLOPT
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
- 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[] )
+   double fret;
+   double *xt;
- {
+   int j;
-   /* Covariances of health expectancies eij and of total life expectancies according
+   myfunc_data *d2 = (myfunc_data *) pd;
-    to initial status i, ei. .
+ /* xt = (p1-1); */
-   */
+   xt=vector(1,n);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   double age, agelim, hf;
-   double ***p3matp, ***p3matm, ***varhe;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-   double **dnewm,**doldm;
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-   double *xp, *xm;
+   printf("Function = %.12lf ",fret);
-   double **gp, **gm;
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   double ***gradg, ***trgradg;
+   printf("\n");
-   int theta;
+  free_vector(xt,1,n);
+   return fret;
-   double eip, vip;
+ }
+ #endif
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   xp=vector(1,npar);
+ /*************** log-likelihood *************/
-   xm=vector(1,npar);
+ double func( double *x)
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+ {
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
-   pstamp(ficresstdeij);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   double **out;
-   fprintf(ficresstdeij,"# Age");
+   double lli; /* Individual log likelihood */
-   for(i=1; i<=nlstate;i++){
+   int s1, s2;
-     for(j=1; j<=nlstate;j++)
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   double bbh, survp;
-     fprintf(ficresstdeij," e%1d. ",i);
+   long ipmx;
-   }
+   double agexact;
-   fprintf(ficresstdeij,"\n");
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
-   pstamp(ficrescveij);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   /*for(i=1;i<imx;i++)
-   fprintf(ficrescveij,"# Age");
+     printf(" %d\n",s[4][i]);
-   for(i=1; i<=nlstate;i++)
+   */
-     for(j=1; j<=nlstate;j++){
-       cptj= (j-1)*nlstate+i;
+   ++countcallfunc;
-       for(i2=1; i2<=nlstate;i2++)
-         for(j2=1; j2<=nlstate;j2++){
+   cov[1]=1.;
-           cptj2= (j2-1)*nlstate+i2;
-           if(cptj2 <= cptj)
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+   ioffset=0;
-         }
+   if(mle==1){
-     }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficrescveij,"\n");
+       /* Computes the values of the ncovmodel covariates of the model
+          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
-   if(estepm < stepm){
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+          to be observed in j being in i according to the model.
-   }
+       */
-   else  hstepm=estepm;
+       ioffset=2+nagesqr+cptcovage;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
-    * This is mainly to measure the difference between two models: for example
+       for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+                                 cov[++ioffset]=covar[Tvar[k]][i];
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       }
-    * progression in between and thus overestimating or underestimating according
+       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
-    * to the curvature of the survival function. If, for the same date, we
+                                 cov[++ioffset]=coqvar[Tvar[iqv]][i];
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+       }
-    * to compare the new estimate of Life expectancy with the same linear
-    * hypothesis. A more precise result, taking into account a more precise
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-    * curvature will be obtained if estepm is as small as stepm. */
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+       /* For an individual i, wav[i] gives the number of effective waves */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       /* We compute the contribution to Likelihood of each effective transition
-      nhstepm is the number of hstepm from age to agelim
+          mw[mi][i] is real wave of the mi th effectve wave */
-      nstepm is the number of stepm from age to agelin.
+       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
-      Look at hpijx to understand the reason of that which relies in memory size
+          s2=s[mw[mi+1][i]][i];
-      and note for a fixed period like estepm months */
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
-      survival function given by stepm (the optimization length). Unfortunately it
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
-      means that if the survival funtion is printed only each two years of age and if
+       */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       for(mi=1; mi<= wav[i]-1; mi++){
-      results. So we changed our mind and took the option of the best precision.
+                                 for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
-   */
+                                         /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+                                         cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
+                                 }
-   /* If stepm=6 months */
+                                 for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
-   /* nhstepm age range expressed in number of stepm */
+                                         if(cotqvar[mw[mi][i]][iqtv][i] == -1){
-   agelim=AGESUP;
+                                                 printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+                                         }
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+                                         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
-   /* if (stepm >= YEARM) hstepm=1;*/
+                                         /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+                                 }
+                                 /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                 for (ii=1;ii<=nlstate+ndeath;ii++)
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                         for (j=1;j<=nlstate+ndeath;j++){
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+                                         }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+                                 for(d=0; d<dh[mi][i]; d++){
+                                         newm=savm;
-   for (age=bage; age<=fage; age ++){
+                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+                                         cov[2]=agexact;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+                                         if(nagesqr==1)
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+                                                 cov[3]= agexact*agexact;  /* Should be changed here */
+                                         for (kk=1; kk<=cptcovage;kk++) {
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+                                         }
-     /* Computing  Variances of health expectancies */
+                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-        decrease memory allocation */
+                                         savm=oldm;
-     for(theta=1; theta <=npar; theta++){
+                                         oldm=newm;
-       for(i=1; i<=npar; i++){
+                                 } /* end mult */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+                                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-       }
+                                 /* But now since version 0.9 we anticipate for bias at large stepm.
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+                                  * If stepm is larger than one month (smallest stepm) and if the exact delay
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+                                  * (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(j=1; j<= nlstate; j++){
+                                  * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         for(i=1; i<=nlstate; i++){
+                                  * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-           for(h=0; h<=nhstepm-1; h++){
+                                  * probability in order to take into account the bias as a fraction of the way
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+                                  * -stepm/2 to stepm/2 .
-           }
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
-         }
+                                  * For stepm > 1 the results are less biased than in previous versions.
-       }
+                                  */
+                                 s1=s[mw[mi][i]][i];
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+                                 s2=s[mw[mi+1][i]][i];
-         for(h=0; h<=nhstepm-1; h++){
+                                 bbh=(double)bh[mi][i]/(double)stepm;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+                                 /* bias bh is positive if real duration
-         }
+                                  * is higher than the multiple of stepm and negative otherwise.
-     }/* End theta */
+                                  */
+                                 /* 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){
-     for(h=0; h<=nhstepm-1; h++)
+                                         /* i.e. if s2 is a death state and if the date of death is known
-       for(j=1; j<=nlstate*nlstate;j++)
+                                                  then the contribution to the likelihood is the probability to
-         for(theta=1; theta <=npar; theta++)
+                                                  die between last step unit time and current  step unit time,
-           trgradg[h][j][theta]=gradg[h][theta][j];
+                                                  which is also equal to probability to die before dh
+                                                  minus probability to die before dh-stepm .
+                                                  In version up to 0.92 likelihood was computed
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+                                                  as if date of death was unknown. Death was treated as any other
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+                                                  health state: the date of the interview describes the actual state
-         varhe[ij][ji][(int)age] =0.;
+                                                  and not the date of a change in health state. The former idea was
+                                                  to consider that at each interview the state was recorded
-      printf("%d|",(int)age);fflush(stdout);
+                                                  (healthy, disable or death) and IMaCh was corrected; but when we
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+                                                  introduced the exact date of death then we should have modified
-      for(h=0;h<=nhstepm-1;h++){
+                                                  the contribution of an exact death to the likelihood. This new
-       for(k=0;k<=nhstepm-1;k++){
+                                                  contribution is smaller and very dependent of the step unit
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+                                                  stepm. It is no more the probability to die between last interview
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+                                                  and month of death but the probability to survive from last
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+                                                  interview up to one month before death multiplied by the
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+                                                  probability to die within a month. Thanks to Chris
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+                                                  Jackson for correcting this bug.  Former versions increased
-       }
+                                                  mortality artificially. The bad side is that we add another loop
-     }
+                                                  which slows down the processing. The difference can be up to 10%
+                                                  lower mortality.
-     /* Computing expectancies */
+                                         */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+                                         /* If, at the beginning of the maximization mostly, the
-     for(i=1; i<=nlstate;i++)
+                                                  cumulative probability or probability to be dead is
-       for(j=1; j<=nlstate;j++)
+                                                  constant (ie = 1) over time d, the difference is equal to
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+.  out[s1][3] = savm[s1][3]: probability, being at state
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+                                                  s1 at precedent wave, to be dead a month before current
+                                                  wave is equal to probability, being at state s1 at
-           /* 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]);*/
+                                                  precedent wave, to be dead at mont of the current
+                                                  wave. Then the observed probability (that this person died)
-         }
+                                                  is null according to current estimated parameter. In fact,
+                                                  it should be very low but not zero otherwise the log go to
-     fprintf(ficresstdeij,"%3.0f",age );
+                                                  infinity.
-     for(i=1; i<=nlstate;i++){
+                                         */
-       eip=0.;
+ /* #ifdef INFINITYORIGINAL */
-       vip=0.;
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-       for(j=1; j<=nlstate;j++){
+ /* #else */
-         eip += eij[i][j][(int)age];
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ /*          lli=log(mytinydouble); */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ /*        else */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-       }
+ /* #endif */
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     }
-     fprintf(ficresstdeij,"\n");
+         } else if  ( s2==-1 ) { /* alive */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-     fprintf(ficrescveij,"%3.0f",age );
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     for(i=1; i<=nlstate;i++)
+           /*survp += out[s1][j]; */
-       for(j=1; j<=nlstate;j++){
+           lli= log(survp);
-         cptj= (j-1)*nlstate+i;
+         }
-         for(i2=1; i2<=nlstate;i2++)
+         else if  (s2==-4) {
-           for(j2=1; j2<=nlstate;j2++){
+           for (j=3,survp=0. ; j<=nlstate; j++)
-             cptj2= (j2-1)*nlstate+i2;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-             if(cptj2 <= cptj)
+           lli= log(survp);
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+         }
-           }
+         else if  (s2==-5) {
-       }
+           for (j=1,survp=0. ; j<=2; j++)
-     fprintf(ficrescveij,"\n");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
-   }
+         }
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+         else{
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+           /*  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 */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+         }
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /*if(lli ==000.0)*/
-   printf("\n");
+         /*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); */
-   fprintf(ficlog,"\n");
+         ipmx +=1;
+         sw += weight[i];
-   free_vector(xm,1,npar);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   free_vector(xp,1,npar);
+         /* if (lli < log(mytinydouble)){ */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+         /*   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); */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+         /*   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]); */
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+         /* } */
- }
+       } /* end of wave */
+     } /* end of individual */
- /************ Variance ******************/
+   }  else if(mle==2){
- 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[])
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- {
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   /* Variance of health expectancies */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   /* double **newm;*/
+           for (j=1;j<=nlstate+ndeath;j++){
-   double **dnewm,**doldm;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double **dnewmp,**doldmp;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int i, j, nhstepm, hstepm, h, nstepm ;
+           }
-   int k, cptcode;
+         for(d=0; d<=dh[mi][i]; d++){
-   double *xp;
+           newm=savm;
-   double **gp, **gm;  /* for var eij */
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   double ***gradg, ***trgradg; /*for var eij */
+           cov[2]=agexact;
-   double **gradgp, **trgradgp; /* for var p point j */
+           if(nagesqr==1)
-   double *gpp, *gmp; /* for var p point j */
+             cov[3]= agexact*agexact;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+           for (kk=1; kk<=cptcovage;kk++) {
-   double ***p3mat;
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   double age,agelim, hf;
+           }
-   double ***mobaverage;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   int theta;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   char digit[4];
+           savm=oldm;
-   char digitp[25];
+           oldm=newm;
+         } /* end mult */
-   char fileresprobmorprev[FILENAMELENGTH];
+         s1=s[mw[mi][i]][i];
-   if(popbased==1){
+         s2=s[mw[mi+1][i]][i];
-     if(mobilav!=0)
+         bbh=(double)bh[mi][i]/(double)stepm;
-       strcpy(digitp,"-populbased-mobilav-");
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-     else strcpy(digitp,"-populbased-nomobil-");
+         ipmx +=1;
-   }
+         sw += weight[i];
-   else
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     strcpy(digitp,"-stablbased-");
+       } /* end of wave */
+     } /* end of individual */
-   if (mobilav!=0) {
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       for(mi=1; mi<= wav[i]-1; mi++){
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     }
+           for (j=1;j<=nlstate+ndeath;j++){
-   }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   strcpy(fileresprobmorprev,"prmorprev");
+           }
-   sprintf(digit,"%-d",ij);
+         for(d=0; d<dh[mi][i]; d++){
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+           newm=savm;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+           cov[2]=agexact;
-   strcat(fileresprobmorprev,fileres);
+           if(nagesqr==1)
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+             cov[3]= agexact*agexact;
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+           for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   }
+           }
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           savm=oldm;
-   pstamp(ficresprobmorprev);
+           oldm=newm;
-   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);
+         } /* end mult */
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+         s1=s[mw[mi][i]][i];
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+         s2=s[mw[mi+1][i]][i];
-     for(i=1; i<=nlstate;i++)
+         bbh=(double)bh[mi][i]/(double)stepm;
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+         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;
-   fprintf(ficresprobmorprev,"\n");
+         sw += weight[i];
-   fprintf(ficgp,"\n# Routine varevsij");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+       } /* end of wave */
-   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");
+     } /* end of individual */
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
- /*   } */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   pstamp(ficresvij);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   if(popbased==1)
+           for (j=1;j<=nlstate+ndeath;j++){
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   else
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+           }
-   fprintf(ficresvij,"# Age");
+         for(d=0; d<dh[mi][i]; d++){
-   for(i=1; i<=nlstate;i++)
+           newm=savm;
-     for(j=1; j<=nlstate;j++)
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+           cov[2]=agexact;
-   fprintf(ficresvij,"\n");
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-   xp=vector(1,npar);
+           for (kk=1; kk<=cptcovage;kk++) {
-   dnewm=matrix(1,nlstate,1,npar);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   doldm=matrix(1,nlstate,1,nlstate);
+           }
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+           savm=oldm;
-   gpp=vector(nlstate+1,nlstate+ndeath);
+           oldm=newm;
-   gmp=vector(nlstate+1,nlstate+ndeath);
+         } /* end mult */
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+         s1=s[mw[mi][i]][i];
-   if(estepm < stepm){
+         s2=s[mw[mi+1][i]][i];
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         if( s2 > nlstate){
-   }
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   else  hstepm=estepm;
+         } else if  ( s2==-1 ) { /* alive */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+             survp += out[s1][j];
-      nhstepm is the number of hstepm from age to agelim
+           lli= log(survp);
-      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
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-      and note for a fixed period like k years */
+         }
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+         ipmx +=1;
-      survival function given by stepm (the optimization length). Unfortunately it
+         sw += weight[i];
-      means that if the survival funtion is printed every two years of age and if
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+ /*      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]); */
-      results. So we changed our mind and took the option of the best precision.
+       } /* end of wave */
-   */
+     } /* end of individual */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   agelim = AGESUP;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       for(mi=1; mi<= wav[i]-1; mi++){
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           for (j=1;j<=nlstate+ndeath;j++){
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     gp=matrix(0,nhstepm,1,nlstate);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     gm=matrix(0,nhstepm,1,nlstate);
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-     for(theta=1; theta <=npar; theta++){
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+           cov[2]=agexact;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           if(nagesqr==1)
-       }
+             cov[3]= agexact*agexact;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+           for (kk=1; kk<=cptcovage;kk++) {
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           }
-       if (popbased==1) {
-         if(mobilav ==0){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           for(i=1; i<=nlstate;i++)
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-             prlim[i][i]=probs[(int)age][i][ij];
+           savm=oldm;
-         }else{ /* mobilav */
+           oldm=newm;
-           for(i=1; i<=nlstate;i++)
+         } /* end mult */
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+         s1=s[mw[mi][i]][i];
-       }
+         s2=s[mw[mi+1][i]][i];
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       for(j=1; j<= nlstate; j++){
+         ipmx +=1;
-         for(h=0; h<=nhstepm; h++){
+         sw += weight[i];
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-         }
+       } /* end of wave */
-       }
+     } /* end of individual */
-       /* This for computing probability of death (h=1 means
+   } /* End of if */
-          computed over hstepm matrices product = hstepm*stepm months)
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-          as a weighted average of prlim.
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   return -l;
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+ }
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+ /*************** log-likelihood *************/
-       /* end probability of death */
+ double funcone( double *x)
+ {
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+   /* Same as func but slower because of a lot of printf and if */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   int i, ii, j, k, mi, d, kk;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   int ioffset=0;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
-       if (popbased==1) {
+   double lli; /* Individual log likelihood */
-         if(mobilav ==0){
+   double llt;
-           for(i=1; i<=nlstate;i++)
+   int s1, s2;
-             prlim[i][i]=probs[(int)age][i][ij];
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+   double bbh, survp;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   double agexact;
-         }
+   double agebegin, ageend;
-       }
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
-       for(j=1; j<= nlstate; j++){
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         for(h=0; h<=nhstepm; h++){
+   /*for(i=1;i<imx;i++)
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+     printf(" %d\n",s[4][i]);
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+   */
-         }
+   cov[1]=1.;
-       }
-       /* This for computing probability of death (h=1 means
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-          computed over hstepm matrices product = hstepm*stepm months)
+   ioffset=0;
-          as a weighted average of prlim.
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       */
+     ioffset=2+nagesqr+cptcovage;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+     /* Fixed */
-         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 (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
-       }
+     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
-       /* end probability of death */
+       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)*/
+ /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
-       for(j=1; j<= nlstate; j++) /* vareij */
+ /*    cov[2+6]=covar[Tvar[6]][i];  */
-         for(h=0; h<=nhstepm; h++){
+ /*    cov[2+6]=covar[2][i]; V2  */
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
-         }
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
-       }
+ /*    cov[2+9]=covar[1][i]; V1  */
+     }
-     } /* End theta */
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
+     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
-     for(h=0; h<=nhstepm; h++) /* veij */
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
-       for(j=1; j<=nlstate;j++)
+     /* } */
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+     /* Wave varying (but not age varying) */
+     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-       for(theta=1; theta <=npar; theta++)
+                                 cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarFind[k]]][i];
-         trgradgp[j][theta]=gradgp[theta][j];
+                         }
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
+                                 /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+                                 /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
-     for(i=1;i<=nlstate;i++)
+                                 /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
-       for(j=1;j<=nlstate;j++)
+                                 /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
-         vareij[i][j][(int)age] =0.;
+                                 /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
-     for(h=0;h<=nhstepm;h++){
+                         /*      iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-       for(k=0;k<=nhstepm;k++){
+                         /*      /\* 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]); *\/ */
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+                         /*      cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+       /* } */
-         for(i=1;i<=nlstate;i++)
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-           for(j=1;j<=nlstate;j++)
+                                 for (j=1;j<=nlstate+ndeath;j++){
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+                                         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       }
+                                         savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     }
+                                 }
-     /* pptj */
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+                                 /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+                                         and mw[mi+1][i]. dh depends on stepm.*/
-         varppt[j][i]=doldmp[j][i];
+                                 newm=savm;
-     /* end ppptj */
+                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     /*  x centered again */
+                                 cov[2]=agexact;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+                                 if(nagesqr==1)
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+                                         cov[3]= agexact*agexact;
+                                 for (kk=1; kk<=cptcovage;kk++) {
-     if (popbased==1) {
+                                         cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-       if(mobilav ==0){
+                                 }
-         for(i=1; i<=nlstate;i++)
+                                 /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
-           prlim[i][i]=probs[(int)age][i][ij];
+                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-       }else{ /* mobilav */
+                                 out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         for(i=1; i<=nlstate;i++)
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-       }
+                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-     }
+                                 savm=oldm;
+                                 oldm=newm;
-     /* This for computing probability of death (h=1 means
+       } /* end mult */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
+       s1=s[mw[mi][i]][i];
-     */
+       s2=s[mw[mi+1][i]][i];
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       /* if(s2==-1){ */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       /*        /\* exit(1); *\/ */
-     }
+       /* } */
-     /* end probability of death */
+       bbh=(double)bh[mi][i]/(double)stepm;
+       /* bias is positive if real duration
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+        * is higher than the multiple of stepm and negative otherwise.
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+        */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-       for(i=1; i<=nlstate;i++){
+                                 lli=log(out[s1][s2] - savm[s1][s2]);
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       } else if  ( s2==-1 ) { /* alive */
-       }
+                                 for (j=1,survp=0. ; j<=nlstate; j++)
-     }
+                                         survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     fprintf(ficresprobmorprev,"\n");
+                                 lli= log(survp);
+       }else if (mle==1){
-     fprintf(ficresvij,"%.0f ",age );
+                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     for(i=1; i<=nlstate;i++)
+       } else if(mle==2){
-       for(j=1; j<=nlstate;j++){
+                                 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 */
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+       } else if(mle==3){  /* exponential inter-extrapolation */
-       }
+                                 lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-     fprintf(ficresvij,"\n");
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     free_matrix(gp,0,nhstepm,1,nlstate);
+                                 lli=log(out[s1][s2]); /* Original formula */
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       } else{  /* mle=0 back to 1 */
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+                                 /*lli=log(out[s1][s2]); */ /* Original formula */
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* End of if */
-   } /* End age */
+       ipmx +=1;
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+       sw += weight[i];
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+       /*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]); */
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+       if(globpr){
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+                                 fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+  %11.6f %11.6f %11.6f ", \
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+                                                                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+                                 for(k=1,llt=0.,l=0.; k<=nlstate; k++){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+                                         llt +=ll[k]*gipmx/gsw;
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+                                         fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+                                 }
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+                                 fprintf(ficresilk," %10.6f\n", -llt);
-   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);
+         } /* end of wave */
-   /*  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);
+ } /* end of individual */
- */
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ if(globpr==0){ /* First time we count the contributions and weights */
-   free_vector(xp,1,npar);
+         gipmx=ipmx;
-   free_matrix(doldm,1,nlstate,1,nlstate);
+         gsw=sw;
-   free_matrix(dnewm,1,nlstate,1,npar);
+ }
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ return -l;
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+ }
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
+ /*************** function likelione ***********/
-   fflush(ficgp);
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-   fflush(fichtm);
+ {
- }  /* end varevsij */
+   /* This routine should help understanding what is done with
+      the selection of individuals/waves and
- /************ Variance of prevlim ******************/
+      to check the exact contribution to the likelihood.
- 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[])
+      Plotting could be done.
- {
+    */
-   /* Variance of prevalence limit */
+   int k;
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-   double **dnewm,**doldm;
+     strcpy(fileresilk,"ILK_");
-   int i, j, nhstepm, hstepm;
+     strcat(fileresilk,fileresu);
-   int k, cptcode;
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-   double *xp;
+       printf("Problem with resultfile: %s\n", fileresilk);
-   double *gp, *gm;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   double **gradg, **trgradg;
+     }
-   double age,agelim;
+     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");
-   int theta;
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-   pstamp(ficresvpl);
+     for(k=1; k<=nlstate; k++)
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   fprintf(ficresvpl,"# Age");
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   for(i=1; i<=nlstate;i++)
+   }
-       fprintf(ficresvpl," %1d-%1d",i,i);
-   fprintf(ficresvpl,"\n");
+   *fretone=(*funcone)(p);
+   if(*globpri !=0){
-   xp=vector(1,npar);
+     fclose(ficresilk);
-   dnewm=matrix(1,nlstate,1,npar);
+     if (mle ==0)
-   doldm=matrix(1,nlstate,1,nlstate);
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
+     else if(mle >=1)
-   hstepm=1*YEARM; /* Every year of age */
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     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));
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     for (k=1; k<= nlstate ; k++) {
-     if (stepm >= YEARM) hstepm=1;
+       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> \
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
-     gradg=matrix(1,npar,1,nlstate);
+     }
-     gp=vector(1,nlstate);
+     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> \
-     gm=vector(1,nlstate);
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
-     for(theta=1; theta <=npar; theta++){
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     fflush(fichtm);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   }
-       }
+   return;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ }
-       for(i=1;i<=nlstate;i++)
-         gp[i] = prlim[i][i];
+ /*********** Maximum Likelihood Estimation ***************/
-       for(i=1; i<=npar; i++) /* Computes gradient */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ {
-       for(i=1;i<=nlstate;i++)
+   int i,j, iter=0;
-         gm[i] = prlim[i][i];
+   double **xi;
+   double fret;
-       for(i=1;i<=nlstate;i++)
+   double fretone; /* Only one call to likelihood */
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   /*  char filerespow[FILENAMELENGTH];*/
-     } /* End theta */
+ #ifdef NLOPT
-     trgradg =matrix(1,nlstate,1,npar);
+   int creturn;
+   nlopt_opt opt;
-     for(j=1; j<=nlstate;j++)
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-       for(theta=1; theta <=npar; theta++)
+   double *lb;
-         trgradg[j][theta]=gradg[theta][j];
+   double minf; /* the minimum objective value, upon return */
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-     for(i=1;i<=nlstate;i++)
+   myfunc_data dinst, *d = &dinst;
-       varpl[i][(int)age] =0.;
+ #endif
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-     for(i=1;i<=nlstate;i++)
+   xi=matrix(1,npar,1,npar);
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   for (i=1;i<=npar;i++)
+     for (j=1;j<=npar;j++)
-     fprintf(ficresvpl,"%.0f ",age );
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     for(i=1; i<=nlstate;i++)
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   strcpy(filerespow,"POW_");
-     fprintf(ficresvpl,"\n");
+   strcat(filerespow,fileres);
-     free_vector(gp,1,nlstate);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     free_vector(gm,1,nlstate);
+     printf("Problem with resultfile: %s\n", filerespow);
-     free_matrix(gradg,1,npar,1,nlstate);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     free_matrix(trgradg,1,nlstate,1,npar);
+   }
-   } /* End age */
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   for (i=1;i<=nlstate;i++)
-   free_vector(xp,1,npar);
+     for(j=1;j<=nlstate+ndeath;j++)
-   free_matrix(doldm,1,nlstate,1,npar);
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   fprintf(ficrespow,"\n");
+ #ifdef POWELL
- }
+   powell(p,xi,npar,ftol,&iter,&fret,func);
+ #endif
- /************ Variance of one-step probabilities  ******************/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+ #ifdef NLOPT
- {
+ #ifdef NEWUOA
-   int i, j=0,  i1, k1, l1, t, tj;
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-   int k2, l2, j1,  z1;
+ #else
-   int k=0,l, cptcode;
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-   int first=1, first1;
+ #endif
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   lb=vector(0,npar-1);
-   double **dnewm,**doldm;
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-   double *xp;
+   nlopt_set_lower_bounds(opt, lb);
-   double *gp, *gm;
+   nlopt_set_initial_step1(opt, 0.1);
-   double **gradg, **trgradg;
-   double **mu;
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   double age,agelim, cov[NCOVMAX];
+   d->function = func;
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   int theta;
+   nlopt_set_min_objective(opt, myfunc, d);
-   char fileresprob[FILENAMELENGTH];
+   nlopt_set_xtol_rel(opt, ftol);
-   char fileresprobcov[FILENAMELENGTH];
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-   char fileresprobcor[FILENAMELENGTH];
+     printf("nlopt failed! %d\n",creturn);
+   }
-   double ***varpij;
+   else {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   strcpy(fileresprob,"prob");
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-   strcat(fileresprob,fileres);
+     iter=1; /* not equal */
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   }
-     printf("Problem with resultfile: %s\n", fileresprob);
+   nlopt_destroy(opt);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+ #endif
-   }
+   free_matrix(xi,1,npar,1,npar);
-   strcpy(fileresprobcov,"probcov");
+   fclose(ficrespow);
-   strcat(fileresprobcov,fileres);
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   }
+ }
-   strcpy(fileresprobcor,"probcor");
-   strcat(fileresprobcor,fileres);
+ /**** Computes Hessian and covariance matrix ***/
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+ {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   double  **a,**y,*x,pd;
-   }
+   /* double **hess; */
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   int i, j;
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   int *indx;
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   pstamp(ficresprob);
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   double gompertz(double p[]);
-   fprintf(ficresprob,"# Age");
+   /* hess=matrix(1,npar,1,npar); */
-   pstamp(ficresprobcov);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-   fprintf(ficresprobcov,"# Age");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-   pstamp(ficresprobcor);
+   for (i=1;i<=npar;i++){
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+     printf("%d-",i);fflush(stdout);
-   fprintf(ficresprobcor,"# Age");
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+     /*  printf(" %f ",p[i]);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   }
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+   for (i=1;i<=npar;i++) {
-  /* fprintf(ficresprob,"\n");
+     for (j=1;j<=npar;j++)  {
-   fprintf(ficresprobcov,"\n");
+       if (j>i) {
-   fprintf(ficresprobcor,"\n");
+         printf(".%d-%d",i,j);fflush(stdout);
-  */
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-  xp=vector(1,npar);
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+         hess[j][i]=hess[i][j];
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+         /*printf(" %lf ",hess[i][j]);*/
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+       }
-   first=1;
+     }
-   fprintf(ficgp,"\n# Routine varprob");
+   }
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   printf("\n");
-   fprintf(fichtm,"\n");
+   fprintf(ficlog,"\n");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-   file %s<br>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   a=matrix(1,npar,1,npar);
- and drawn. It helps understanding how is the covariance between two incidences.\
+   y=matrix(1,npar,1,npar);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   x=vector(1,npar);
-   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. \
+   indx=ivector(1,npar);
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   for (i=1;i<=npar;i++)
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
- standard deviations wide on each axis. <br>\
+   ludcmp(a,npar,indx,&pd);
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   for (j=1;j<=npar;j++) {
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     for (i=1;i<=npar;i++) x[i]=0;
+     x[j]=1;
-   cov[1]=1;
+     lubksb(a,npar,indx,x);
-   tj=cptcoveff;
+     for (i=1;i<=npar;i++){
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+       matcov[i][j]=x[i];
-   j1=0;
+     }
-   for(t=1; t<=tj;t++){
+   }
-     for(i1=1; i1<=ncodemax[t];i1++){
-       j1++;
+   printf("\n#Hessian matrix#\n");
-       if  (cptcovn>0) {
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-         fprintf(ficresprob, "\n#********** Variable ");
+   for (i=1;i<=npar;i++) {
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     for (j=1;j<=npar;j++) {
-         fprintf(ficresprob, "**********\n#\n");
+       printf("%.6e ",hess[i][j]);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+       fprintf(ficlog,"%.6e ",hess[i][j]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     }
-         fprintf(ficresprobcov, "**********\n#\n");
+     printf("\n");
+     fprintf(ficlog,"\n");
-         fprintf(ficgp, "\n#********** Variable ");
+   }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficgp, "**********\n#\n");
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+   /*   for (j=1;j<=npar;j++) {  */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   /*     printf("%.6e ",matcov[i][j]); */
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   /*   printf("\n"); */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   /*   fprintf(ficlog,"\n"); */
-         fprintf(ficresprobcor, "**********\n#");
+   /* } */
-       }
+   /* Recompute Inverse */
-       for (age=bage; age<=fage; age ++){
+   /* for (i=1;i<=npar;i++) */
-         cov[2]=age;
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-         for (k=1; k<=cptcovn;k++) {
+   /* ludcmp(a,npar,indx,&pd); */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
-         }
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (k=1; k<=cptcovprod;k++)
+   /* for (j=1;j<=npar;j++) { */
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   /*   lubksb(a,npar,indx,x); */
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   /*   for (i=1;i<=npar;i++){  */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+   /*     y[i][j]=x[i]; */
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
-         for(theta=1; theta <=npar; theta++){
+   /*   } */
-           for(i=1; i<=npar; i++)
+   /*   printf("\n"); */
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   /* Verifying the inverse matrix */
-           k=0;
+ #ifdef DEBUGHESS
-           for(i=1; i<= (nlstate); i++){
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
-               gp[k]=pmmij[i][j];
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
-             }
-           }
+   for (j=1;j<=npar;j++) {
+     for (i=1;i<=npar;i++){
-           for(i=1; i<=npar; i++)
+       printf("%.2f ",y[i][j]);
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+       fprintf(ficlog,"%.2f ",y[i][j]);
+     }
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     printf("\n");
-           k=0;
+     fprintf(ficlog,"\n");
-           for(i=1; i<=(nlstate); i++){
+   }
-             for(j=1; j<=(nlstate+ndeath);j++){
+ #endif
-               k=k+1;
-               gm[k]=pmmij[i][j];
+   free_matrix(a,1,npar,1,npar);
-             }
+   free_matrix(y,1,npar,1,npar);
-           }
+   free_vector(x,1,npar);
+   free_ivector(indx,1,npar);
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+   /* free_matrix(hess,1,npar,1,npar); */
-             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++)
+ /*************** hessian matrix ****************/
-             trgradg[j][theta]=gradg[theta][j];
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+   int i;
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+   int l=1, lmax=20;
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   double k1,k2, res, fx;
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   double p2[MAXPARM+1]; /* identical to x */
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   int k=0,kmax=10;
+   double l1;
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+   fx=func(x);
-         k=0;
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-         for(i=1; i<=(nlstate); i++){
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-           for(j=1; j<=(nlstate+ndeath);j++){
+     l1=pow(10,l);
-             k=k+1;
+     delts=delt;
-             mu[k][(int) age]=pmmij[i][j];
+     for(k=1 ; k <kmax; k=k+1){
-           }
+       delt = delta*(l1*k);
-         }
+       p2[theta]=x[theta] +delt;
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+       p2[theta]=x[theta]-delt;
-             varpij[i][j][(int)age] = doldm[i][j];
+       k2=func(p2)-fx;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-         /*printf("\n%d ",(int)age);
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
-           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]));
+ #ifdef DEBUGHESSII
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-           }*/
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+ #endif
-         fprintf(ficresprob,"\n%d ",(int)age);
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+         k=kmax;
+       }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         k=kmax; l=lmax*10;
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+       }
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         delts=delt;
-         }
+       }
-         i=0;
+     } /* End loop k */
-         for (k=1; k<=(nlstate);k++){
+   }
-           for (l=1; l<=(nlstate+ndeath);l++){
+   delti[theta]=delts;
-             i=i++;
+   return res;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+ }
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+ {
-             }
+   int i;
-           }
+   int l=1, lmax=20;
-         }/* end of loop for state */
+   double k1,k2,k3,k4,res,fx;
-       } /* end of loop for age */
+   double p2[MAXPARM+1];
+   int k, kmax=1;
-       /* Confidence intervalle of pij  */
+   double v1, v2, cv12, lc1, lc2;
-       /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+   int firstime=0;
-         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");
+   fx=func(x);
-         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);
+   for (k=1; k<=kmax; k=k+10) {
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-       */
+     k1=func(p2)-fx;
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-       first1=1;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-       for (k2=1; k2<=(nlstate);k2++){
+     k2=func(p2)-fx;
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-           j=(k2-1)*(nlstate+ndeath)+l2;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-           for (k1=1; k1<=(nlstate);k1++){
+     k3=func(p2)-fx;
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-               if(i<=j) continue;
+     k4=func(p2)-fx;
-               for (age=bage; age<=fage; age ++){
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
-                 if ((int)age %5==0){
+     if(k1*k2*k3*k4 <0.){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+       firstime=1;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+       kmax=kmax+10;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     }
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+     if(kmax >=10 || firstime ==1){
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
-                   c12=cv12/sqrt(v1*v2);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
-                   /* Computing eigen value of matrix of covariance */
+       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);
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       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);
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     }
-                   /* Eigen vectors */
+ #ifdef DEBUGHESSIJ
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     v1=hess[thetai][thetai];
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+     v2=hess[thetaj][thetaj];
-                   v21=(lc1-v1)/cv12*v11;
+     cv12=res;
-                   v12=-v21;
+     /* Computing eigen value of Hessian matrix */
-                   v22=v11;
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   tnalp=v21/v11;
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   if(first1==1){
+     if ((lc2 <0) || (lc1 <0) ){
-                     first1=0;
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-                     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, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-                   }
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-                   fprintf(ficlog,"%d %d%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);
+       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(fignu*/
+     }
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+ #endif
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+   }
-                   if(first==1){
+   return res;
-                     first=0;
+ }
-                     fprintf(ficgp,"\nset parametric;unset label");
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+ /* { */
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+ /*   int i; */
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+ /*   int l=1, lmax=20; */
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+ /*   double k1,k2,k3,k4,res,fx; */
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ /*   double p2[MAXPARM+1]; */
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ /*   int k=0,kmax=10; */
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ /*   double l1; */
-                     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);
+ /*   fx=func(x); */
-                     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(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+ /*     l1=pow(10,l); */
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ /*     delts=delt; */
-                   }else{
+ /*     for(k=1 ; k <kmax; k=k+1){ */
-                     first=0;
+ /*       delt = delti*(l1*k); */
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+ /*       k1=func(p2)-fx; */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-                   }/* if first */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-                 } /* age mod 5 */
+ /*       k2=func(p2)-fx; */
-               } /* end loop age */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-               first=1;
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-             } /*l12 */
+ /*       k3=func(p2)-fx; */
-           } /* k12 */
-         } /*l1 */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-       }/* k1 */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-     } /* loop covariates */
+ /*       k4=func(p2)-fx; */
-   }
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+ /* #ifdef DEBUGHESSIJ */
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+ /*       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); */
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ /*       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); */
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+ /* #endif */
-   free_vector(xp,1,npar);
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
-   fclose(ficresprob);
+ /*      k=kmax; */
-   fclose(ficresprobcov);
+ /*       } */
-   fclose(ficresprobcor);
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
-   fflush(ficgp);
+ /*      k=kmax; l=lmax*10; */
-   fflush(fichtmcov);
+ /*       } */
- }
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
+ /*      delts=delt; */
+ /*       } */
- /******************* Printing html file ***********/
+ /*     } /\* End loop k *\/ */
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ /*   } */
-                   int lastpass, int stepm, int weightopt, char model[],\
+ /*   delti[theta]=delts; */
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+ /*   return res;  */
-                   int popforecast, int estepm ,\
+ /* } */
-                   double jprev1, double mprev1,double anprev1, \
-                   double jprev2, double mprev2,double anprev2){
-   int jj1, k1, i1, cpt;
+ /************** Inverse of matrix **************/
+ void ludcmp(double **a, int n, int *indx, double *d)
-    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 \
+   int i,imax,j,k;
- </ul>");
+   double big,dum,sum,temp;
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   double *vv;
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   vv=vector(1,n);
-    fprintf(fichtm,"\
+   *d=1.0;
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   for (i=1;i<=n;i++) {
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+     big=0.0;
-    fprintf(fichtm,"\
+     for (j=1;j<=n;j++)
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-    fprintf(fichtm,"\
+     vv[i]=1.0/big;
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+   }
-    <a href=\"%s\">%s</a> <br>\n",
+   for (j=1;j<=n;j++) {
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+     for (i=1;i<j;i++) {
-    fprintf(fichtm,"\
+       sum=a[i][j];
-  - Population projections by age and states: \
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+       a[i][j]=sum;
+     }
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+     big=0.0;
+     for (i=j;i<=n;i++) {
-  m=cptcoveff;
+       sum=a[i][j];
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       for (k=1;k<j;k++)
+         sum -= a[i][k]*a[k][j];
-  jj1=0;
+       a[i][j]=sum;
-  for(k1=1; k1<=m;k1++){
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-    for(i1=1; i1<=ncodemax[k1];i1++){
+         big=dum;
-      jj1++;
+         imax=i;
-      if (cptcovn > 0) {
+       }
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     }
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+     if (j != imax) {
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       for (k=1;k<=n;k++) {
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+         dum=a[imax][k];
-      }
+         a[imax][k]=a[j][k];
-      /* Pij */
+         a[j][k]=dum;
-      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);
+       *d = -(*d);
-      /* Quasi-incidences */
+       vv[imax]=vv[j];
-      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> \
+     indx[j]=imax;
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-        /* Period (stable) prevalence in each health state */
+     if (j != n) {
-        for(cpt=1; cpt<nlstate;cpt++){
+       dum=1.0/(a[j][j]);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+     }
-        }
+   }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   free_vector(vv,1,n);  /* Doesn't work */
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+ ;
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ }
-      }
-    } /* end i1 */
+ void lubksb(double **a, int n, int *indx, double b[])
-  }/* End k1 */
+ {
-  fprintf(fichtm,"</ul>");
+   int i,ii=0,ip,j;
+   double sum;
-  fprintf(fichtm,"\
+   for (i=1;i<=n;i++) {
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+     ip=indx[i];
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+     sum=b[ip];
+     b[ip]=b[i];
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     if (ii)
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-  fprintf(fichtm,"\
+     else if (sum) ii=i;
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     b[i]=sum;
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   }
+   for (i=n;i>=1;i--) {
-  fprintf(fichtm,"\
+     sum=b[i];
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+     b[i]=sum/a[i][i];
-  fprintf(fichtm,"\
+   }
-  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+ }
-    <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+ void pstamp(FILE *fichier)
-  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): \
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+ }
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-  fprintf(fichtm,"\
+ /************ Frequencies ********************/
-  - 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",
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
-  fprintf(fichtm,"\
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-  - 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",
+ {  /* Some frequencies */
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-  fprintf(fichtm,"\
+   int i, m, jk, j1, bool, z1,j, k, iv;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   int iind=0, iage=0;
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   int mi; /* Effective wave */
+   int first;
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   double ***freq; /* Frequencies */
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   double *meanq;
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   double **meanqt;
- /*      <br>",fileres,fileres,fileres,fileres); */
+   double *pp, **prop, *posprop, *pospropt;
- /*  else  */
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
- /*    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); */
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-  fflush(fichtm);
+   double agebegin, ageend;
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   pp=vector(1,nlstate);
-  m=cptcoveff;
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
+   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
-  jj1=0;
+   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
-  for(k1=1; k1<=m;k1++){
+   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   meanqt=matrix(1,lastpass,1,nqtveff);
-      jj1++;
+   strcpy(fileresp,"P_");
-      if (cptcovn > 0) {
+   strcat(fileresp,fileresu);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   /*strcat(fileresphtm,fileresu);*/
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-      }
+     exit(0);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   }
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
-      }
+     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
- health expectancies in states (1) and (2): %s%d.png<br>\
+     fflush(ficlog);
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+     exit(70);
-    } /* end i1 */
+   }
-  }/* End k1 */
+   else{
-  fprintf(fichtm,"</ul>");
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-  fflush(fichtm);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
- }
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+             fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
- /******************* Gnuplot file **************/
+   }
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
-   char dirfileres[132],optfileres[132];
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
-   int ng;
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
- /*     printf("Problem with file %s",optionfilegnuplot); */
+     fflush(ficlog);
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+     exit(70);
- /*   } */
+   }
+   else{
-   /*#ifdef windows */
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     /*#endif */
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
-   m=pow(2,cptcoveff);
+             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
-   strcpy(dirfileres,optionfilefiname);
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
-   strcpy(optfileres,"vpl");
-  /* 1eme*/
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   j1=0;
-    for (k1=1; k1<= m ; k1 ++) {
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+   j=cptcoveff;  /* Only dummy covariates of the model */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
- set ylabel \"Probability\" \n\
- set ter png small\n\
+   first=1;
- set size 0.65,0.65\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
+      reference=low_education V1=0,V2=0
-      for (i=1; i<= nlstate ; i ++) {
+      med_educ                V1=1 V2=0,
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+      high_educ               V1=0 V2=1
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
-      }
+   */
-      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);
-      for (i=1; i<= nlstate ; i ++) {
+   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+     posproptt=0.;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-      }
+       scanf("%d", i);*/
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+     for (i=-5; i<=nlstate+ndeath; i++)
-      for (i=1; i<= nlstate ; i ++) {
+       for (jk=-5; jk<=nlstate+ndeath; jk++)
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+                                 for(m=iagemin; m <= iagemax+3; m++)
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                         freq[i][jk][m]=0;
-      }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+     for (i=1; i<=nlstate; i++)  {
-    }
+       for(m=iagemin; m <= iagemax+3; m++)
-   }
+                                 prop[i][m]=0;
-   /*2 eme*/
+       posprop[i]=0;
+       pospropt[i]=0;
-   for (k1=1; k1<= m ; k1 ++) {
+     }
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+     /* for (z1=1; z1<= nqfveff; z1++) {   */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+     /*   meanq[z1]+=0.; */
+     /*   for(m=1;m<=lastpass;m++){ */
-     for (i=1; i<= nlstate+1 ; i ++) {
+     /*  meanqt[m][z1]=0.; */
-       k=2*i;
+     /*   } */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     /* } */
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+     dateintsum=0;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+     k2cpt=0;
-       }
+     /* For that combination of covariate j1, we count and print the frequencies in one pass */
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+       bool=1;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                 if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           /* for (z1=1; z1<= nqfveff; z1++) {   */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-       }
+           /* } */
-       fprintf(ficgp,"\" t\"\" w l 0,");
+                                         for (z1=1; z1<=cptcoveff; z1++) {
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                 /* if(Tvaraff[z1] ==-20){ */
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                                                 /* }else  if(Tvaraff[z1] ==-10){ */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-       }
+                                                 /* }else  */
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+                                                         /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
-     }
+                                                         bool=0;
-   }
+                                                         /* 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",
+                                                                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-   /*3eme*/
+                                                                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+                                                         /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-   for (k1=1; k1<= m ; k1 ++) {
+                                                 } /* Onlyf fixed */
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+                                         } /* end z1 */
-       /*       k=2+nlstate*(2*cpt-2); */
+                                 } /* cptcovn > 0 */
-       k=2+(nlstate+1)*(cpt-1);
+       } /* end any */
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
-       fprintf(ficgp,"set ter png small\n\
+                                 /* for(m=firstpass; m<=lastpass; m++){ */
- set size 0.65,0.65\n\
+                                 for(mi=1; mi<wav[iind];mi++){ /* For that wave */
- 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);
+                                         m=mw[mi][iind];
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                                         if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                                 for (z1=1; z1<=cptcoveff; z1++) {
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                                                         if( Fixed[Tmodelind[z1]]==1){
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                                                                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                                                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                                                                         bool=0;
+                                                         }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-       */
+                                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-       for (i=1; i< nlstate ; i ++) {
+                                                                         bool=0;
-         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);*/
+                                                         }
+                                                 }
-       }
+                                         }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+                                         /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-     }
+                                         if(bool==1){
-   }
+                                                 /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                                                          and mw[mi+1][iind]. dh depends on stepm. */
-   /* CV preval stable (period) */
+                                                 agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-   for (k1=1; k1<= m ; k1 ++) {
+                                                 ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+                                                 if(m >=firstpass && m <=lastpass){
-       k=3;
+                                                         k2=anint[m][iind]+(mint[m][iind]/12.);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+                                                         /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+                                                         if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
- set ter png small\nset size 0.65,0.65\n\
+                                                         if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
- unset log y\n\
+                                                         if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+                                                                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+                                                         if (m<lastpass) {
-       for (i=1; i< nlstate ; i ++)
+                                                                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-         fprintf(ficgp,"+$%d",k+i+1);
+                                                                 /*   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]); */
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+                                                                 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.));
-       l=3+(nlstate+ndeath)*cpt;
+                                                                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+                                                                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-       for (i=1; i< nlstate ; i ++) {
+                                                                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
-         l=3+(nlstate+ndeath)*cpt;
+                                                         }
-         fprintf(ficgp,"+$%d",l+i+1);
+                                                 } /* end if between passes */
-       }
+                                                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+                                                         dateintsum=dateintsum+k2;
-     }
+                                                         k2cpt++;
-   }
+                                                         /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+                                                 }
-   /* proba elementaires */
+                                         } /* end bool 2 */
-   for(i=1,jk=1; i <=nlstate; i++){
+                                 } /* end m */
-     for(k=1; k <=(nlstate+ndeath); k++){
+       } /* end bool */
-       if (k != i) {
+     } /* end iind = 1 to imx */
-         for(j=1; j <=ncovmodel; j++){
+     /* prop[s][age] is feeded for any initial and valid live state as well as
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
-           jk++;
-           fprintf(ficgp,"\n");
-         }
+     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       }
+     pstamp(ficresp);
-     }
+     /* if  (ncoveff>0) { */
-    }
+     if  (cptcoveff>0) {
+       fprintf(ficresp, "\n#********** Variable ");
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-      for(jk=1; jk <=m; jk++) {
+       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+       for (z1=1; z1<=cptcoveff; z1++){
-        if (ng==2)
+                                 fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+                                 fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-        else
+                                 fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+       }
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       fprintf(ficresp, "**********\n#");
-        i=1;
+       fprintf(ficresphtm, "**********</h3>\n");
-        for(k2=1; k2<=nlstate; k2++) {
+       fprintf(ficresphtmfr, "**********</h3>\n");
-          k3=i;
+       fprintf(ficlog, "\n#********** Variable ");
-          for(k=1; k<=(nlstate+ndeath); k++) {
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-            if (k != k2){
+       fprintf(ficlog, "**********\n");
-              if(ng==2)
+     }
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-              else
+     for(i=1; i<=nlstate;i++) {
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-              ij=1;
+       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-              for(j=3; j <=ncovmodel; j++) {
+     }
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     fprintf(ficresp, "\n");
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+     fprintf(ficresphtm, "\n");
-                  ij++;
-                }
+     /* Header of frequency table by age */
-                else
+     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     fprintf(ficresphtmfr,"<th>Age</th> ");
-              }
+     for(jk=-1; jk <=nlstate+ndeath; jk++){
-              fprintf(ficgp,")/(1");
+       for(m=-1; m <=nlstate+ndeath; m++){
+                                 if(jk!=0 && m!=0)
-              for(k1=1; k1 <=nlstate; k1++){
+                                         fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+       }
-                ij=1;
+     }
-                for(j=3; j <=ncovmodel; j++){
+     fprintf(ficresphtmfr, "\n");
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+     /* For each age */
-                    ij++;
+     for(iage=iagemin; iage <= iagemax+3; iage++){
-                  }
+       fprintf(ficresphtm,"<tr>");
-                  else
+       if(iage==iagemax+1){
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                                 fprintf(ficlog,"1");
-                }
+                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
-                fprintf(ficgp,")");
+       }else if(iage==iagemax+2){
-              }
+                                 fprintf(ficlog,"0");
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+       }else if(iage==iagemax+3){
-              i=i+ncovmodel;
+                                 fprintf(ficlog,"Total");
-            }
+                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-          } /* end k */
+       }else{
-        } /* end k2 */
+                                 if(first==1){
-      } /* end jk */
+                                         first=0;
-    } /* end ng */
+                                         printf("See log file for details...\n");
-    fflush(ficgp);
+                                 }
- }  /* end gnuplot */
+                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+                                 fprintf(ficlog,"Age %d", iage);
+       }
- /*************** Moving average **************/
+       for(jk=1; jk <=nlstate ; jk++){
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+                                         pp[jk] += freq[jk][m][iage];
-   int i, cpt, cptcod;
+       }
-   int modcovmax =1;
+       for(jk=1; jk <=nlstate ; jk++){
-   int mobilavrange, mob;
+                                 for(m=-1, pos=0; m <=0 ; m++)
-   double age;
+                                         pos += freq[jk][m][iage];
+                                 if(pp[jk]>=1.e-10){
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                                         if(first==1){
-                            a covariate has 2 modalities */
+                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                                         }
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+                                 }else{
-     if(mobilav==1) mobilavrange=5; /* default */
+                                         if(first==1)
-     else mobilavrange=mobilav;
+                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     for (age=bage; age<=fage; age++)
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-       for (i=1; i<=nlstate;i++)
+                                 }
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+       }
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-     /* We keep the original values on the extreme ages bage, fage and for
+       for(jk=1; jk <=nlstate ; jk++){
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                                 /* posprop[jk]=0; */
-        we use a 5 terms etc. until the borders are no more concerned.
+                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-     */
+                                         pp[jk] += freq[jk][m][iage];
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-         for (i=1; i<=nlstate;i++){
+       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-               }
+       }
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+       for(jk=1; jk <=nlstate ; jk++){
-           }
+                                 if(pos>=1.e-5){
-         }
+                                         if(first==1)
-       }/* end age */
+                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-     }/* end mob */
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   }else return -1;
+                                 }else{
-   return 0;
+                                         if(first==1)
- }/* End movingaverage */
+                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                 }
- /************** Forecasting ******************/
+                                 if( iage <= iagemax){
- 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){
+                                         if(pos>=1.e-5){
-   /* proj1, year, month, day of starting projection
+                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-      agemin, agemax range of age
+                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
-      anproj2 year of en of projection (same day and month as proj1).
+                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
-   */
+                                         }
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+                                         else{
-   int *popage;
+                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
-   double agec; /* generic age */
+                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+                                         }
-   double *popeffectif,*popcount;
+                                 }
-   double ***p3mat;
+                                 pospropt[jk] +=posprop[jk];
-   double ***mobaverage;
+       } /* end loop jk */
-   char fileresf[FILENAMELENGTH];
+       /* pospropt=0.; */
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
-   agelim=AGESUP;
+                                 for(m=-1; m <=nlstate+ndeath; m++){
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                                                 if(first==1){
-   strcpy(fileresf,"f");
+                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-   strcat(fileresf,fileres);
+                                                 }
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+                                         }
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+                                         if(jk!=0 && m!=0)
-   }
+                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+                                 }
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+       } /* end loop jk */
+       posproptt=0.;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+       for(jk=1; jk <=nlstate; jk++){
+                                 posproptt += pospropt[jk];
-   if (mobilav!=0) {
+       }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficresphtmfr,"</tr>\n ");
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       if(iage <= iagemax){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                                 fprintf(ficresp,"\n");
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                                 fprintf(ficresphtm,"</tr>\n");
-     }
+       }
-   }
+       if(first==1)
+                                 printf("Others in log...\n");
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+       fprintf(ficlog,"\n");
-   if (stepm<=12) stepsize=1;
+     } /* end loop age iage */
-   if(estepm < stepm){
+     fprintf(ficresphtm,"<tr><th>Tot</th>");
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+     for(jk=1; jk <=nlstate ; jk++){
-   }
+       if(posproptt < 1.e-5){
-   else  hstepm=estepm;
+                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+       }else{
-   hstepm=hstepm/stepm;
+                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+       }
-                                fractional in yp1 */
+     }
-   anprojmean=yp;
+     fprintf(ficresphtm,"</tr>\n");
-   yp2=modf((yp1*12),&yp);
+     fprintf(ficresphtm,"</table>\n");
-   mprojmean=yp;
+     fprintf(ficresphtmfr,"</table>\n");
-   yp1=modf((yp2*30.5),&yp);
+     if(posproptt < 1.e-5){
-   jprojmean=yp;
+       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-   if(jprojmean==0) jprojmean=1;
+       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-   if(mprojmean==0) jprojmean=1;
+       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+       invalidvarcomb[j1]=1;
-   i1=cptcoveff;
+     }else{
-   if (cptcovn < 1){i1=1;}
+       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+       invalidvarcomb[j1]=0;
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+     }
+     fprintf(ficresphtmfr,"</table>\n");
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   } /* end selected combination of covariate j1 */
+   dateintmean=dateintsum/k2cpt;
- /*            if (h==(int)(YEARM*yearp)){ */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   fclose(ficresp);
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   fclose(ficresphtm);
-       k=k+1;
+   fclose(ficresphtmfr);
-       fprintf(ficresf,"\n#******");
+   free_vector(meanq,1,nqfveff);
-       for(j=1;j<=cptcoveff;j++) {
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
-         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]]);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
-       }
+   free_vector(pospropt,1,nlstate);
-       fprintf(ficresf,"******\n");
+   free_vector(posprop,1,nlstate);
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
-       for(j=1; j<=nlstate+ndeath;j++){
+   free_vector(pp,1,nlstate);
-         for(i=1; i<=nlstate;i++)
+   /* End of freqsummary */
-           fprintf(ficresf," p%d%d",i,j);
+ }
-         fprintf(ficresf," p.%d",j);
-       }
+ /************ Prevalence ********************/
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+ 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)
-         fprintf(ficresf,"\n");
+ {
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   /* 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).
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+      We still use firstpass and lastpass as another selection.
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+   */
-           nhstepm = nhstepm/hstepm;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int i, m, jk, j1, bool, z1,j, iv;
-           oldm=oldms;savm=savms;
+   int mi; /* Effective wave */
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+   int iage;
+   double agebegin, ageend;
-           for (h=0; h<=nhstepm; h++){
-             if (h*hstepm/YEARM*stepm ==yearp) {
+   double **prop;
-               fprintf(ficresf,"\n");
+   double posprop;
-               for(j=1;j<=cptcoveff;j++)
+   double  y2; /* in fractional years */
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   int iagemin, iagemax;
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+   int first; /** to stop verbosity which is redirected to log file */
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
+   iagemin= (int) agemin;
-               ppij=0.;
+   iagemax= (int) agemax;
-               for(i=1; i<=nlstate;i++) {
+   /*pp=vector(1,nlstate);*/
-                 if (mobilav==1)
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-                 else {
+   j1=0;
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-                 }
+   /*j=cptcoveff;*/
-                 if (h*hstepm/YEARM*stepm== yearp) {
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
+   first=1;
-               } /* end i */
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-               if (h*hstepm/YEARM*stepm==yearp) {
+     for (i=1; i<=nlstate; i++)
-                 fprintf(ficresf," %.3f", ppij);
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-               }
+         prop[i][iage]=0.0;
-             }/* end j */
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-           } /* end h */
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-         } /* end agec */
-       } /* end yearp */
+     for (i=1; i<=imx; i++) { /* Each individual */
-     } /* end cptcod */
+       bool=1;
-   } /* end  cptcov */
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         m=mw[mi][i];
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
-   fclose(ficresf);
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
- }
+         for (z1=1; z1<=cptcoveff; z1++){
+           if( Fixed[Tmodelind[z1]]==1){
- /************** Forecasting *****not tested NB*************/
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
- 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 (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
+               bool=0;
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-   int *popage;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-   double calagedatem, agelim, kk1, kk2;
+               bool=0;
-   double *popeffectif,*popcount;
+             }
-   double ***p3mat,***tabpop,***tabpopprev;
+         }
-   double ***mobaverage;
+         if(bool==1){ /* Otherwise we skip that wave/person */
-   char filerespop[FILENAMELENGTH];
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           if(m >=firstpass && m <=lastpass){
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   agelim=AGESUP;
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
+                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
+                 exit(1);
-   strcpy(filerespop,"pop");
+               }
-   strcat(filerespop,fileres);
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+                 /*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("Problem with forecast resultfile: %s\n", filerespop);
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   }
+               } /* end valid statuses */
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+             } /* end selection of dates */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+           } /* end selection of waves */
+         } /* end bool */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+       } /* end wave */
+     } /* end individual */
-   if (mobilav!=0) {
+     for(i=iagemin; i <= iagemax+3; i++){
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+         posprop += prop[jk][i];
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       }
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
+       for(jk=1; jk <=nlstate ; jk++){
-   }
+         if( i <=  iagemax){
+           if(posprop>=1.e-5){
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-   if (stepm<=12) stepsize=1;
+           } else{
+             if(first==1){
-   agelim=AGESUP;
+               first=0;
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
-   hstepm=1;
+             }
-   hstepm=hstepm/stepm;
+           }
+         }
-   if (popforecast==1) {
+       }/* end jk */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+     }/* end i */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+      /*} *//* end i1 */
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+   } /* end j1 */
-     }
-     popage=ivector(0,AGESUP);
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-     popeffectif=vector(0,AGESUP);
+   /*free_vector(pp,1,nlstate);*/
-     popcount=vector(0,AGESUP);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+ }  /* End of prevalence */
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /************* Waves Concatenation ***************/
-     imx=i;
+ 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)
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ {
-   }
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+      Death is a valid wave (if date is known).
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-       k=k+1;
+      and mw[mi+1][i]. dh depends on stepm.
-       fprintf(ficrespop,"\n#******");
+   */
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   int i=0, mi=0, m=0, mli=0;
-       }
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-       fprintf(ficrespop,"******\n");
+      double sum=0., jmean=0.;*/
-       fprintf(ficrespop,"# Age");
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+   int j, k=0,jk, ju, jl;
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+   double sum=0.;
+   first=0;
-       for (cpt=0; cpt<=0;cpt++) {
+   firstwo=0;
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   firsthree=0;
+   firstfour=0;
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+   jmin=100000;
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   jmax=-1;
-           nhstepm = nhstepm/hstepm;
+   jmean=0.;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /* Treating live states */
-           oldm=oldms;savm=savms;
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     mi=0;  /* First valid wave */
+     mli=0; /* Last valid wave */
-           for (h=0; h<=nhstepm; h++){
+     m=firstpass;
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+     while(s[m][i] <= nlstate){  /* a live state */
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
-             }
+         mli=m-1;/* mw[++mi][i]=m-1; */
-             for(j=1; j<=nlstate+ndeath;j++) {
+       }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 */
-               kk1=0.;kk2=0;
+         mw[++mi][i]=m;
-               for(i=1; i<=nlstate;i++) {
+         mli=m;
-                 if (mobilav==1)
+       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+       if(m < lastpass){ /* m < lastpass, standard case */
-                 else {
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+       }
-                 }
+       else{ /* m >= lastpass, eventual special issue with warning */
-               }
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
-               if (h==(int)(calagedatem+12*cpt)){
+         break;
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+ #else
-                   /*fprintf(ficrespop," %.3f", kk1);
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+           if(firsthree == 0){
-               }
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\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);
-             }
+             firsthree=1;
-             for(i=1; i<=nlstate;i++){
+           }
-               kk1=0.;
+           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 pi. .\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);
-                 for(j=1; j<=nlstate;j++){
+           mw[++mi][i]=m;
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+           mli=m;
-                 }
+         }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+         if(s[m][i]==-2){ /* Vital status is really unknown */
-             }
+           nbwarn++;
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+             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);
            }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           break;
          }
-       }
+         break;
+ #endif
-   /******/
+       }/* End m >= lastpass */
+     }/* end while */
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     /* After last pass */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /* Treating death states */
-           nhstepm = nhstepm/hstepm;
+     if (s[m][i] > nlstate){  /* In a death state */
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* } */
-           oldm=oldms;savm=savms;
+       mi++;     /* Death is another wave */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       /* if(mi==0)  never been interviewed correctly before death */
-           for (h=0; h<=nhstepm; h++){
+       /* Only death is a correct wave */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       mw[mi][i]=m;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+     }
-             }
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-             for(j=1; j<=nlstate+ndeath;j++) {
+     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
-               kk1=0.;kk2=0;
+       /* m++; */
-               for(i=1; i<=nlstate;i++) {
+       /* mi++; */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
-               }
+       /* mw[mi][i]=m; */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-             }
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
-           }
+           nbwarn++;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           if(firstfiv==0){
-         }
+             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 );
-       }
+             firstfiv=1;
-    }
+           }else{
-   }
+             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 );
+           }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         }else{ /* Death occured afer last wave potential bias */
+           nberr++;
-   if (popforecast==1) {
+           if(firstwo==0){
-     free_ivector(popage,0,AGESUP);
+             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.\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 );
-     free_vector(popeffectif,0,AGESUP);
+             firstwo=1;
-     free_vector(popcount,0,AGESUP);
+           }
-   }
+           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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         }
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       }else{ /* end date of interview is known */
-   fclose(ficrespop);
+         /* death is known but not confirmed by death status at any wave */
- } /* End of popforecast */
+         if(firstfour==0){
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. 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 );
- int fileappend(FILE *fichier, char *optionfich)
+           firstfour=1;
- {
+         }
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+         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 );
-     printf("Problem with file: %s\n", optionfich);
+       }
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     } /* end if date of death is known */
-     return (0);
+ #endif
-   }
+     wav[i]=mi; /* mi should be the last effective wave (or mli) */
-   fflush(fichier);
+     /* wav[i]=mw[mi][i]; */
-   return (1);
+     if(mi==0){
- }
+       nbwarn++;
+       if(first==0){
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
- /**************** function prwizard **********************/
+         first=1;
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+       }
- {
+       if(first==1){
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-   /* Wizard to print covariance matrix template */
+       }
+     } /* end mi==0 */
-   char ca[32], cb[32], cc[32];
+   } /* End individuals */
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   /* wav and mw are no more changed */
-   int numlinepar;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(i=1; i<=imx; i++){
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(mi=1; mi<wav[i];mi++){
-   for(i=1; i <=nlstate; i++){
+       if (stepm <=0)
-     jj=0;
+         dh[mi][i]=1;
-     for(j=1; j <=nlstate+ndeath; j++){
+       else{
-       if(j==i) continue;
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-       jj++;
+           if (agedc[i] < 2*AGESUP) {
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-       printf("%1d%1d",i,j);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-       fprintf(ficparo,"%1d%1d",i,j);
+             else if(j<0){
-       for(k=1; k<=ncovmodel;k++){
+               nberr++;
-         /*        printf(" %lf",param[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]);
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+               j=1; /* Temporary Dangerous patch */
-         printf(" 0.");
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-         fprintf(ficparo," 0.");
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-       }
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-       printf("\n");
+             }
-       fprintf(ficparo,"\n");
+             k=k+1;
-     }
+             if (j >= jmax){
-   }
+               jmax=j;
-   printf("# Scales (for hessian or gradient estimation)\n");
+               ijmax=i;
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+             }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+             if (j <= jmin){
-   for(i=1; i <=nlstate; i++){
+               jmin=j;
-     jj=0;
+               ijmin=i;
-     for(j=1; j <=nlstate+ndeath; j++){
+             }
-       if(j==i) continue;
+             sum=sum+j;
-       jj++;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-       fprintf(ficparo,"%1d%1d",i,j);
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-       printf("%1d%1d",i,j);
+           }
-       fflush(stdout);
+         }
-       for(k=1; k<=ncovmodel;k++){
+         else{
-         /*      printf(" %le",delti3[i][j][k]); */
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+ /*        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]); */
-         printf(" 0.");
-         fprintf(ficparo," 0.");
+           k=k+1;
-       }
+           if (j >= jmax) {
-       numlinepar++;
+             jmax=j;
-       printf("\n");
+             ijmax=i;
-       fprintf(ficparo,"\n");
+           }
-     }
+           else if (j <= jmin){
-   }
+             jmin=j;
-   printf("# Covariance matrix\n");
+             ijmin=i;
- /* # 121 Var(a12)\n\ */
+           }
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+           /*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]);*/
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+           if(j<0){
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+             nberr++;
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+             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]);
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+             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]);
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+           }
-   fflush(stdout);
+           sum=sum+j;
-   fprintf(ficparo,"# Covariance matrix\n");
+         }
-   /* # 121 Var(a12)\n\ */
+         jk= j/stepm;
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+         jl= j -jk*stepm;
-   /* #   ...\n\ */
+         ju= j -(jk+1)*stepm;
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+           if(jl==0){
-   for(itimes=1;itimes<=2;itimes++){
+             dh[mi][i]=jk;
-     jj=0;
+             bh[mi][i]=0;
-     for(i=1; i <=nlstate; i++){
+           }else{ /* We want a negative bias in order to only have interpolation ie
-       for(j=1; j <=nlstate+ndeath; j++){
+                   * to avoid the price of an extra matrix product in likelihood */
-         if(j==i) continue;
+             dh[mi][i]=jk+1;
-         for(k=1; k<=ncovmodel;k++){
+             bh[mi][i]=ju;
-           jj++;
+           }
-           ca[0]= k+'a'-1;ca[1]='\0';
+         }else{
-           if(itimes==1){
+           if(jl <= -ju){
-             printf("#%1d%1d%d",i,j,k);
+             dh[mi][i]=jk;
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+             bh[mi][i]=jl;       /* bias is positive if real duration
-           }else{
+                                  * is higher than the multiple of stepm and negative otherwise.
-             printf("%1d%1d%d",i,j,k);
+                                  */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+           }
-             /*  printf(" %.5le",matcov[i][j]); */
+           else{
-           }
+             dh[mi][i]=jk+1;
-           ll=0;
+             bh[mi][i]=ju;
-           for(li=1;li <=nlstate; li++){
+           }
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+           if(dh[mi][i]==0){
-               if(lj==li) continue;
+             dh[mi][i]=1; /* At least one step */
-               for(lk=1;lk<=ncovmodel;lk++){
+             bh[mi][i]=ju; /* At least one step */
-                 ll++;
+             /*  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);*/
-                 if(ll<=jj){
+           }
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+         } /* end if mle */
-                   if(ll<jj){
+       }
-                     if(itimes==1){
+     } /* end wave */
-                       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);
+   jmean=sum/k;
-                     }else{
+   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);
-                       printf(" 0.");
+   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);
-                       fprintf(ficparo," 0.");
+ }
-                     }
-                   }else{
+ /*********** Tricode ****************************/
-                     if(itimes==1){
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+ {
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-                     }else{
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-                       printf(" 0.");
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-                       fprintf(ficparo," 0.");
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-                     }
+    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
-                   }
+   */
-                 }
-               } /* end lk */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-             } /* end lj */
+   int modmaxcovj=0; /* Modality max of covariates j */
-           } /* end li */
+   int cptcode=0; /* Modality max of covariates j */
-           printf("\n");
+   int modmincovj=0; /* Modality min of covariates j */
-           fprintf(ficparo,"\n");
-           numlinepar++;
-         } /* end k*/
+   /* cptcoveff=0;  */
-       } /*end j */
+         /* *cptcov=0; */
-     } /* end i */
-   } /* end itimes */
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
- } /* end of prwizard */
+   /* Loop on covariates without age and products and no quantitative variable */
- /******************* Gompertz Likelihood ******************************/
+   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
- double gompertz(double x[])
+   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;
-   double A,B,L=0.0,sump=0.,num=0.;
+     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-   int i,n=0; /* n is the size of the sample */
+       switch(Fixed[k]) {
+       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-   for (i=0;i<=imx-1 ; i++) {
+                                 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*/
-     sump=sump+weight[i];
+                                         ij=(int)(covar[Tvar[k]][i]);
-     /*    sump=sump+1;*/
+                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-     num=num+1;
+                                          * If product of Vn*Vm, still boolean *:
-   }
+                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   /* for (i=0; i<=imx; i++)
+                                                  modality of the nth covariate of individual 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]);*/
+                                         if (ij > modmaxcovj)
+                                                 modmaxcovj=ij;
-   for (i=1;i<=imx ; i++)
+                                         else if (ij < modmincovj)
-     {
+                                                 modmincovj=ij;
-       if (cens[i] == 1 && wav[i]>1)
+                                         if ((ij < -1) && (ij > NCOVMAX)){
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+                                                 exit(1);
-       if (cens[i] == 0 && wav[i]>1)
+                                         }else
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+                                         /* getting the maximum value of the modality of the covariate
-       if (wav[i] > 1 ) { /* ??? */
+                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-         L=L+A*weight[i];
+                                                  female ies 1, then modmaxcovj=1.
-         /*      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]);*/
+                                         */
-       }
+                                 } /* end for loop on individuals i */
-     }
+                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+                                 cptcode=modmaxcovj;
+                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   return -2*L*num/sump;
+                                 /*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 */
+                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
- /******************* Printing html file ***********/
+                                         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-                   int lastpass, int stepm, int weightopt, char model[],\
+                                                 if( j != -1){
-                   int imx,  double p[],double **matcov,double agemortsup){
+                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-   int i,k;
+                                                                                                                                  covariate for which somebody answered excluding
+                                                                                                                                  undefined. Usually 2: 0 and 1. */
-   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);
+                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
-   for (i=1;i<=2;i++)
+                                                                                                                                                 covariate for which somebody answered including
-     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]));
+                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
-   fprintf(fichtm,"</ul>");
+                                                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+                                 } /* Ndum[-1] number of undefined modalities */
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+                                 /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-  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 covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
+                                 /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-  for (k=agegomp;k<(agemortsup-2);k++)
+                                 /* modmincovj=3; modmaxcovj = 7; */
-    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]);
+                                 /* 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; */
+                           /*             defining two dummy variables: variables V1_1 and V1_2.*/
-   fflush(fichtm);
+               /* nbcode[Tvar[j]][ij]=k; */
- }
+               /* nbcode[Tvar[j]][1]=0; */
+               /* nbcode[Tvar[j]][2]=1; */
- /******************* Gnuplot file **************/
+               /* nbcode[Tvar[j]][3]=2; */
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+               /* To be continued (not working yet). */
+               ij=0; /* ij is similar to i but can jump over null modalities */
-   char dirfileres[132],optfileres[132];
+                                 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*/
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-   int ng;
+                   break;
+                 }
+                                         ij++;
-   /*#ifdef windows */
+                                         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*/
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+                                         cptcode = ij; /* New max modality for covar j */
-     /*#endif */
+                                 } /* end of loop on modality i=-1 to 1 or more */
+                                 break;
+       case 1: /* Testing on varying covariate, could be simple and
-   strcpy(dirfileres,optionfilefiname);
+                * should look at waves or product of fixed *
-   strcpy(optfileres,"vpl");
+                * varying. No time to test -1, assuming 0 and 1 only */
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+                                 ij=0;
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+                                 for(i=0; i<=1;i++){
-   fprintf(ficgp, "set ter png small\n set log y\n");
+                                         nbcode[Tvar[k]][++ij]=i;
-   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);
+                                 break;
+       default:
- }
+                                 break;
+       } /* end switch */
+     } /* end dummy test */
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+     /*  /\*recode from 0 *\/ */
- /***********************************************/
+     /*                               k is a modality. If we have model=V1+V1*sex  */
- /**************** Main Program *****************/
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
- /***********************************************/
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+     /*  } */
- int main(int argc, char *argv[])
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
- {
+     /*  if (ij > ncodemax[j]) { */
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-   int linei, month, year,iout;
+     /*    break; */
-   int jj, ll, li, lj, lk, imk;
+     /*  } */
-   int numlinepar=0; /* Current linenumber of parameter file */
+     /*   }  /\* end of loop on modality k *\/ */
-   int itimes;
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   int NDIM=2;
+   for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   char ca[32], cb[32], cc[32];
+   /* Look at fixed dummy (single or product) covariates to check empty modalities */
-   char dummy[]="                         ";
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-   /*  FILE *fichtm; *//* Html File */
+     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-   /* FILE *ficgp;*/ /*Gnuplot File */
+     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 */
-   struct stat info;
+     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 */
-   double agedeb, agefin,hf;
+     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-   double fret;
+   ij=0;
-   double **xi,tmp,delta;
+   /* 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) */
-   double dum; /* Dummy variable */
+     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   double ***p3mat;
+     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-   double ***mobaverage;
+     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-   int *indx;
+       /* If product not in single variable we don't print results */
-   char line[MAXLINE], linepar[MAXLINE];
+       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
-   char pathr[MAXLINE], pathimach[MAXLINE];
+       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*/
-   char **bp, *tok, *val; /* pathtot */
+       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-   int firstobs=1, lastobs=10;
+       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 */
-   int sdeb, sfin; /* Status at beginning and end */
+       if(Fixed[k]!=0)
-   int c,  h , cpt,l;
+         anyvaryingduminmodel=1;
-   int ju,jl, mi;
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
-   int mobilav=0,popforecast=0;
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
-   int hstepm, nhstepm;
+                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
-   int agemortsup;
+     }
-   float  sumlpop=0.;
+   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   /* ij--; */
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+   *cptcov=ij; /*Number of total real effective covariates: effective
-   double bage, fage, age, agelim, agebase;
+                                                          * because they can be excluded from the model and real
-   double ftolpl=FTOL;
+                                                          * if in the model but excluded because missing values, but how to get k from ij?*/
-   double **prlim;
+   for(j=ij+1; j<= cptcovt; j++){
-   double *severity;
+     Tvaraff[j]=0;
-   double ***param; /* Matrix of parameters */
+     Tmodelind[j]=0;
-   double  *p;
+   }
-   double **matcov; /* Matrix of covariance */
+   for(j=ntveff+1; j<= cptcovt; j++){
-   double ***delti3; /* Scale */
+     TmodelInvind[j]=0;
-   double *delti; /* Scale */
+   }
-   double ***eij, ***vareij;
+   /* To be sorted */
-   double **varpl; /* Variances of prevalence limits by age */
+   ;
-   double *epj, vepp;
+ }
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   double **ximort;
+ /*********** Health Expectancies ****************/
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
-   int *dcwave;
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   char z[1]="c", occ;
+ {
+   /* Health expectancies, no variances */
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   int i, j, nhstepm, hstepm, h, nstepm;
-   char  *strt, strtend[80];
+   int nhstepma, nstepma; /* Decreasing with age */
-   char *stratrunc;
+   double age, agelim, hf;
-   int lstra;
+   double ***p3mat;
+   double eip;
-   long total_usecs;
+   pstamp(ficreseij);
- /*   setlocale (LC_ALL, ""); */
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+   fprintf(ficreseij,"# Age");
- /*   textdomain (PACKAGE); */
+   for(i=1; i<=nlstate;i++){
- /*   setlocale (LC_CTYPE, ""); */
+     for(j=1; j<=nlstate;j++){
- /*   setlocale (LC_MESSAGES, ""); */
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+     fprintf(ficreseij," e%1d. ",i);
-   (void) gettimeofday(&start_time,&tzp);
+   }
-   curr_time=start_time;
+   fprintf(ficreseij,"\n");
-   tm = *localtime(&start_time.tv_sec);
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
- /*  printf("Localtime (at start)=%s",strstart); */
+   }
- /*  tp.tv_sec = tp.tv_sec +86400; */
+   else  hstepm=estepm;
- /*  tm = *localtime(&start_time.tv_sec); */
+   /* We compute the life expectancy from trapezoids spaced every estepm months
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+    * This is mainly to measure the difference between two models: for example
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+    * we are calculating an estimate of the Life Expectancy assuming a linear
- /*   tp.tv_sec = mktime(&tmg); */
+    * progression in between and thus overestimating or underestimating according
- /*   strt=asctime(&tmg); */
+    * to the curvature of the survival function. If, for the same date, we
- /*   printf("Time(after) =%s",strstart);  */
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
- /*  (void) time (&time_value);
+    * to compare the new estimate of Life expectancy with the same linear
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+    * hypothesis. A more precise result, taking into account a more precise
- *  tm = *localtime(&time_value);
+    * curvature will be obtained if estepm is as small as stepm. */
- *  strstart=asctime(&tm);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+   /* 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
-   nberr=0; /* Number of errors and warnings */
+      nstepm is the number of stepm from age to agelin.
-   nbwarn=0;
+      Look at hpijx to understand the reason of that which relies in memory size
-   getcwd(pathcd, size);
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   printf("\n%s\n%s",version,fullversion);
+      survival function given by stepm (the optimization length). Unfortunately it
-   if(argc <=1){
+      means that if the survival funtion is printed only each two years of age and if
-     printf("\nEnter the parameter file name: ");
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     fgets(pathr,FILENAMELENGTH,stdin);
+      results. So we changed our mind and took the option of the best precision.
-     i=strlen(pathr);
+   */
-     if(pathr[i-1]=='\n')
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+   agelim=AGESUP;
-       printf("Pathr |%s|\n",pathr);
+   /* If stepm=6 months */
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-       printf("val= |%s| pathr=%s\n",val,pathr);
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-       strcpy (pathtot, val);
-       if(pathr[0] == '\0') break; /* Dirty */
+ /* nhstepm age range expressed in number of stepm */
-     }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   }
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   else{
+   /* if (stepm >= YEARM) hstepm=1;*/
-     strcpy(pathtot,argv[1]);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   }
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-   /*cygwin_split_path(pathtot,path,optionfile);
+   for (age=bage; age<=fage; age ++){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   /* cutv(path,optionfile,pathtot,'\\');*/
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
-   /* Split argv[0], imach program to get pathimach */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     /* If stepm=6 months */
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-  /*   strcpy(pathimach,argv[0]); */
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path); /* Can be a relative path */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-     printf("Current directory %s!\n",pathcd);
+     printf("%d|",(int)age);fflush(stdout);
-   strcpy(command,"mkdir ");
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   strcat(command,optionfilefiname);
-   if((outcmd=system(command)) != 0){
+     /* Computing expectancies */
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     for(i=1; i<=nlstate;i++)
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+       for(j=1; j<=nlstate;j++)
-     /* fclose(ficlog); */
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- /*     exit(1); */
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-   }
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+           /* 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]);*/
- /*     perror("mkdir"); */
- /*   } */
+         }
-   /*-------- arguments in the command line --------*/
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-   /* Log file */
+       eip=0;
-   strcat(filelog, optionfilefiname);
+       for(j=1; j<=nlstate;j++){
-   strcat(filelog,".log");    /* */
+         eip +=eij[i][j][(int)age];
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-     printf("Problem with logfile %s\n",filelog);
+       }
-     goto end;
+       fprintf(ficreseij,"%9.4f", eip );
-   }
+     }
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+     fprintf(ficreseij,"\n");
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   }
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  path=%s \n\
+   printf("\n");
-  optionfile=%s\n\
+   fprintf(ficlog,"\n");
-  optionfilext=%s\n\
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+ }
-   printf("Local time (at start):%s",strstart);
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-   fprintf(ficlog,"Local time (at start): %s",strstart);
-   fflush(ficlog);
+ {
- /*   (void) gettimeofday(&curr_time,&tzp); */
+   /* Covariances of health expectancies eij and of total life expectancies according
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+      to initial status i, ei. .
+   */
-   /* */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   strcpy(fileres,"r");
+   int nhstepma, nstepma; /* Decreasing with age */
-   strcat(fileres, optionfilefiname);
+   double age, agelim, hf;
-   strcat(fileres,".txt");    /* Other files have txt extension */
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
-   /*---------arguments file --------*/
+   double *xp, *xm;
+   double **gp, **gm;
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+   double ***gradg, ***trgradg;
-     printf("Problem with optionfile %s\n",optionfile);
+   int theta;
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-     fflush(ficlog);
+   double eip, vip;
-     goto end;
-   }
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   xp=vector(1,npar);
+   xm=vector(1,npar);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   strcpy(filereso,"o");
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+   pstamp(ficresstdeij);
-     printf("Problem with Output resultfile: %s\n", filereso);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+   fprintf(ficresstdeij,"# Age");
-     fflush(ficlog);
+   for(i=1; i<=nlstate;i++){
-     goto end;
+     for(j=1; j<=nlstate;j++)
-   }
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     fprintf(ficresstdeij," e%1d. ",i);
-   /* Reads comments: lines beginning with '#' */
+   }
-   numlinepar=0;
+   fprintf(ficresstdeij,"\n");
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   pstamp(ficrescveij);
-     fgets(line, MAXLINE, ficpar);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-     numlinepar++;
+   fprintf(ficrescveij,"# Age");
-     puts(line);
+   for(i=1; i<=nlstate;i++)
-     fputs(line,ficparo);
+     for(j=1; j<=nlstate;j++){
-     fputs(line,ficlog);
+       cptj= (j-1)*nlstate+i;
-   }
+       for(i2=1; i2<=nlstate;i2++)
-   ungetc(c,ficpar);
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+           if(cptj2 <= cptj)
-   numlinepar++;
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+         }
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+     }
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficrescveij,"\n");
-   fflush(ficlog);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   if(estepm < stepm){
-     ungetc(c,ficpar);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     fgets(line, MAXLINE, ficpar);
+   }
-     numlinepar++;
+   else  hstepm=estepm;
-     puts(line);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     fputs(line,ficparo);
+    * This is mainly to measure the difference between two models: for example
-     fputs(line,ficlog);
+    * 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
-   ungetc(c,ficpar);
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   covar=matrix(0,NCOVMAX,1,n);
+    * to compare the new estimate of Life expectancy with the same linear
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+    * hypothesis. A more precise result, taking into account a more precise
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+    * curvature will be obtained if estepm is as small as stepm. */
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+      Look at hpijx to understand the reason of that which relies in memory size
-   delti=delti3[1][1];
+      and note for a fixed period like estepm months */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+      survival function given by stepm (the optimization length). Unfortunately it
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+      means that if the survival funtion is printed only each two years of age and if
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+      results. So we changed our mind and took the option of the best precision.
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   */
-     fclose (ficparo);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     fclose (ficlog);
-     goto end;
+   /* If stepm=6 months */
-     exit(0);
+   /* nhstepm age range expressed in number of stepm */
-   }
+   agelim=AGESUP;
-   else if(mle==-3) {
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+   /* if (stepm >= YEARM) hstepm=1;*/
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     matcov=matrix(1,npar,1,npar);
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   else{
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     /* Read guess parameters */
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     /* Reads comments: lines beginning with '#' */
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   for (age=bage; age<=fage; age ++){
-       numlinepar++;
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       puts(line);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       fputs(line,ficparo);
+     /* if (stepm >= YEARM) hstepm=1;*/
-       fputs(line,ficlog);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     }
-     ungetc(c,ficpar);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     for(i=1; i <=nlstate; i++){
-       j=0;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       for(jj=1; jj <=nlstate+ndeath; jj++){
-         if(jj==i) continue;
+     /* Computing  Variances of health expectancies */
-         j++;
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+        decrease memory allocation */
-         if ((i1 != i) && (j1 != j)){
+     for(theta=1; theta <=npar; theta++){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+       for(i=1; i<=npar; i++){
- It might be a problem of design; if ncovcol and the model are correct\n \
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-           exit(1);
+       }
-         }
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-         if(mle==1)
-           printf("%1d%1d",i,j);
+       for(j=1; j<= nlstate; j++){
-         fprintf(ficlog,"%1d%1d",i,j);
+         for(i=1; i<=nlstate; i++){
-         for(k=1; k<=ncovmodel;k++){
+           for(h=0; h<=nhstepm-1; h++){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-           if(mle==1){
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-             printf(" %lf",param[i][j][k]);
+           }
-             fprintf(ficlog," %lf",param[i][j][k]);
+         }
-           }
+       }
-           else
-             fprintf(ficlog," %lf",param[i][j][k]);
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-           fprintf(ficparo," %lf",param[i][j][k]);
+         for(h=0; h<=nhstepm-1; h++){
-         }
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         fscanf(ficpar,"\n");
+         }
-         numlinepar++;
+     }/* End theta */
-         if(mle==1)
-           printf("\n");
-         fprintf(ficlog,"\n");
+     for(h=0; h<=nhstepm-1; h++)
-         fprintf(ficparo,"\n");
+       for(j=1; j<=nlstate*nlstate;j++)
-       }
+         for(theta=1; theta <=npar; theta++)
-     }
+           trgradg[h][j][theta]=gradg[h][theta][j];
-     fflush(ficlog);
-     p=param[1][1];
+     for(ij=1;ij<=nlstate*nlstate;ij++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-     /* Reads comments: lines beginning with '#' */
+         varhe[ij][ji][(int)age] =0.;
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+     printf("%d|",(int)age);fflush(stdout);
-       fgets(line, MAXLINE, ficpar);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       numlinepar++;
+     for(h=0;h<=nhstepm-1;h++){
-       puts(line);
+       for(k=0;k<=nhstepm-1;k++){
-       fputs(line,ficparo);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-       fputs(line,ficlog);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-     }
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-     ungetc(c,ficpar);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-     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){
+     /* Computing expectancies */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-           exit(1);
+     for(i=1; i<=nlstate;i++)
-         }
+       for(j=1; j<=nlstate;j++)
-         printf("%1d%1d",i,j);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-         fprintf(ficparo,"%1d%1d",i1,j1);
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-         fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
+           /* 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]);*/
-           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]);
+     fprintf(ficresstdeij,"%3.0f",age );
-         }
+     for(i=1; i<=nlstate;i++){
-         fscanf(ficpar,"\n");
+       eip=0.;
-         numlinepar++;
+       vip=0.;
-         printf("\n");
+       for(j=1; j<=nlstate;j++){
-         fprintf(ficparo,"\n");
+         eip += eij[i][j][(int)age];
-         fprintf(ficlog,"\n");
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-       }
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-     }
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-     fflush(ficlog);
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-     delti=delti3[1][1];
+     }
+     fprintf(ficresstdeij,"\n");
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     fprintf(ficrescveij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++)
-     /* Reads comments: lines beginning with '#' */
+       for(j=1; j<=nlstate;j++){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         cptj= (j-1)*nlstate+i;
-       ungetc(c,ficpar);
+         for(i2=1; i2<=nlstate;i2++)
-       fgets(line, MAXLINE, ficpar);
+           for(j2=1; j2<=nlstate;j2++){
-       numlinepar++;
+             cptj2= (j2-1)*nlstate+i2;
-       puts(line);
+             if(cptj2 <= cptj)
-       fputs(line,ficparo);
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-       fputs(line,ficlog);
+           }
-     }
+       }
-     ungetc(c,ficpar);
+     fprintf(ficrescveij,"\n");
-     matcov=matrix(1,npar,1,npar);
+   }
-     for(i=1; i <=npar; i++){
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-       fscanf(ficpar,"%s",&str);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-       if(mle==1)
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-         printf("%s",str);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-       fprintf(ficlog,"%s",str);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fprintf(ficparo,"%s",str);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(j=1; j <=i; j++){
+   printf("\n");
-         fscanf(ficpar," %le",&matcov[i][j]);
+   fprintf(ficlog,"\n");
-         if(mle==1){
-           printf(" %.5le",matcov[i][j]);
+   free_vector(xm,1,npar);
-         }
+   free_vector(xp,1,npar);
-         fprintf(ficlog," %.5le",matcov[i][j]);
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-         fprintf(ficparo," %.5le",matcov[i][j]);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-       }
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-       fscanf(ficpar,"\n");
+ }
-       numlinepar++;
-       if(mle==1)
+ /************ Variance ******************/
-         printf("\n");
+  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[])
-       fprintf(ficlog,"\n");
+  {
-       fprintf(ficparo,"\n");
+    /* Variance of health expectancies */
-     }
+    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-     for(i=1; i <=npar; i++)
+    /* double **newm;*/
-       for(j=i+1;j<=npar;j++)
+    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-         matcov[i][j]=matcov[j][i];
+    /* int movingaverage(); */
-     if(mle==1)
+    double **dnewm,**doldm;
-       printf("\n");
+    double **dnewmp,**doldmp;
-     fprintf(ficlog,"\n");
+    int i, j, nhstepm, hstepm, h, nstepm ;
+    int k;
-     fflush(ficlog);
+    double *xp;
+    double **gp, **gm;  /* for var eij */
-     /*-------- Rewriting parameter file ----------*/
+    double ***gradg, ***trgradg; /*for var eij */
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+    double **gradgp, **trgradgp; /* for var p point j */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+    double *gpp, *gmp; /* for var p point j */
-     strcat(rfileres,".");    /* */
+    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+    double ***p3mat;
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+    double age,agelim, hf;
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+    /* double ***mobaverage; */
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+    int theta;
-     }
+    char digit[4];
-     fprintf(ficres,"#%s\n",version);
+    char digitp[25];
-   }    /* End of mle != -3 */
+    char fileresprobmorprev[FILENAMELENGTH];
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+    if(popbased==1){
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+      if(mobilav!=0)
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-   }
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
+    }
-   n= lastobs;
+    else
-   severity = vector(1,maxwav);
+      strcpy(digitp,"-STABLBASED_");
-   outcome=imatrix(1,maxwav+1,1,n);
-   num=lvector(1,n);
+    /* if (mobilav!=0) { */
-   moisnais=vector(1,n);
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   annais=vector(1,n);
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-   moisdc=vector(1,n);
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-   andc=vector(1,n);
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-   agedc=vector(1,n);
+    /*   } */
-   cod=ivector(1,n);
+    /* } */
-   weight=vector(1,n);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+    strcpy(fileresprobmorprev,"PRMORPREV-");
-   mint=matrix(1,maxwav,1,n);
+    sprintf(digit,"%-d",ij);
-   anint=matrix(1,maxwav,1,n);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   s=imatrix(1,maxwav+1,1,n);
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   tab=ivector(1,NCOVMAX);
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   ncodemax=ivector(1,8);
+    strcat(fileresprobmorprev,fileresu);
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   i=1;
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   linei=0;
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+    }
-     linei=linei+1;
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-       if(line[j] == '\t')
+    pstamp(ficresprobmorprev);
-         line[j] = ' ';
+    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-     }
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       ;
+      fprintf(ficresprobmorprev," p.%-d SE",j);
-     };
+      for(i=1; i<=nlstate;i++)
-     line[j+1]=0;  /* Trims blanks at end of line */
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-     if(line[0]=='#'){
+    }
-       fprintf(ficlog,"Comment line\n%s\n",line);
+    fprintf(ficresprobmorprev,"\n");
-       printf("Comment line\n%s\n",line);
-       continue;
+    fprintf(ficgp,"\n# Routine varevsij");
-     }
+    fprintf(ficgp,"\nunset title \n");
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     for (j=maxwav;j>=1;j--){
+    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");
-       cutv(stra, strb,line,' ');
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-       errno=0;
+    /*   } */
-       lval=strtol(strb,&endptr,10);
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+    pstamp(ficresvij);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-         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);
+    if(popbased==1)
-         exit(1);
+      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-       }
+    else
-       s[j][i]=lval;
+      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+    fprintf(ficresvij,"# Age");
-       strcpy(line,stra);
+    for(i=1; i<=nlstate;i++)
-       cutv(stra, strb,line,' ');
+      for(j=1; j<=nlstate;j++)
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-       }
+    fprintf(ficresvij,"\n");
-       else  if(iout=sscanf(strb,"%s.") != 0){
-         month=99;
+    xp=vector(1,npar);
-         year=9999;
+    dnewm=matrix(1,nlstate,1,npar);
-       }else{
+    doldm=matrix(1,nlstate,1,nlstate);
-         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);
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-         exit(1);
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       }
-       anint[j][i]= (double) year;
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-       mint[j][i]= (double)month;
+    gpp=vector(nlstate+1,nlstate+ndeath);
-       strcpy(line,stra);
+    gmp=vector(nlstate+1,nlstate+ndeath);
-     } /* ENd Waves */
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     cutv(stra, strb,line,' ');
+    if(estepm < stepm){
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+      printf ("Problem %d lower than %d\n",estepm, stepm);
-     }
+    }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+    else  hstepm=estepm;
-       month=99;
+    /* For example we decided to compute the life expectancy with the smallest unit */
-       year=9999;
+    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     }else{
+       nhstepm is the number of hstepm from age to agelim
-       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);
+       nstepm is the number of stepm from age to agelim.
-       exit(1);
+       Look at function hpijx to understand why because of memory size limitations,
-     }
+       we decided (b) to get a life expectancy respecting the most precise curvature of the
-     andc[i]=(double) year;
+       survival function given by stepm (the optimization length). Unfortunately it
-     moisdc[i]=(double) month;
+       means that if the survival funtion is printed every two years of age and if
-     strcpy(line,stra);
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       results. So we changed our mind and took the option of the best precision.
-     cutv(stra, strb,line,' ');
+    */
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     }
+    agelim = AGESUP;
-     else  if(iout=sscanf(strb,"%s.") != 0){
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       month=99;
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       year=9999;
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     }else{
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       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);
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-       exit(1);
+      gp=matrix(0,nhstepm,1,nlstate);
-     }
+      gm=matrix(0,nhstepm,1,nlstate);
-     annais[i]=(double)(year);
-     moisnais[i]=(double)(month);
-     strcpy(line,stra);
+      for(theta=1; theta <=npar; theta++){
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-     cutv(stra, strb,line,' ');
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     errno=0;
+        }
-     dval=strtod(strb,&endptr);
-     if( strb[0]=='\0' || (*endptr != '\0')){
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       exit(1);
+        if (popbased==1) {
-     }
+          if(mobilav ==0){
-     weight[i]=dval;
+            for(i=1; i<=nlstate;i++)
-     strcpy(line,stra);
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
-     for (j=ncovcol;j>=1;j--){
+            for(i=1; i<=nlstate;i++)
-       cutv(stra, strb,line,' ');
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-       errno=0;
+          }
-       lval=strtol(strb,&endptr,10);
+        }
-       if( strb[0]=='\0' || (*endptr != '\0')){
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
-         exit(1);
+        for(j=1; j<= nlstate; j++){
-       }
+          for(h=0; h<=nhstepm; h++){
-       if(lval <-1 || lval >1){
+            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-  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 \
+        /* Next for computing probability of death (h=1 means
-  build V1=0 V2=0 for the reference value (1),\n \
+           computed over hstepm matrices product = hstepm*stepm months)
-         V1=1 V2=0 for (2) \n \
+           as a weighted average of prlim.
-  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 \
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-  Exiting.\n",lval,linei, i,line,j);
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
-         exit(1);
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+        }
-       covar[j][i]=(double)(lval);
+        /* end probability of death */
-       strcpy(line,stra);
-     }
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-     lstra=strlen(stra);
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
-       stratrunc = &(stra[lstra-9]);
-       num[i]=atol(stratrunc);
+        if (popbased==1) {
-     }
+          if(mobilav ==0){
-     else
+            for(i=1; i<=nlstate;i++)
-       num[i]=atol(stra);
+              prlim[i][i]=probs[(int)age][i][ij];
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+          }else{ /* mobilav */
-       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=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-     i=i+1;
+          }
-   } /* End loop reading  data */
+        }
-   fclose(fic);
-   /* printf("ii=%d", ij);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
+        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+          for(h=0; h<=nhstepm; h++){
-   /* for (i=1; i<=imx; i++){
+            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+          }
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+        }
-     }*/
+        /* This for computing probability of death (h=1 means
-    /*  for (i=1; i<=imx; i++){
+           computed over hstepm matrices product = hstepm*stepm months)
-      if (s[4][i]==9)  s[4][i]=-1;
+           as a weighted average of prlim.
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   /* for (i=1; i<=imx; i++) */
+          for(i=1,gmp[j]=0.; i<= nlstate; i++)
+            gmp[j] += prlim[i][i]*p3mat[i][j][1];
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+        }
-      else weight[i]=1;*/
+        /* end probability of death */
-   /* Calculation of the number of parameters from char model */
+        for(j=1; j<= nlstate; j++) /* vareij */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+          for(h=0; h<=nhstepm; h++){
-   Tprod=ivector(1,15);
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   Tvaraff=ivector(1,15);
+          }
-   Tvard=imatrix(1,15,1,2);
-   Tage=ivector(1,15);
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+        }
-     j=0, j1=0, k1=1, k2=1;
-     j=nbocc(model,'+'); /* j=Number of '+' */
+      } /* End theta */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
-     cptcovn=j+1;
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     cptcovprod=j1; /*Number of products */
+      for(h=0; h<=nhstepm; h++) /* veij */
-     strcpy(modelsav,model);
+        for(j=1; j<=nlstate;j++)
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+          for(theta=1; theta <=npar; theta++)
-       printf("Error. Non available option model=%s ",model);
+            trgradg[h][j][theta]=gradg[h][theta][j];
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
-       goto end;
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-     }
+        for(theta=1; theta <=npar; theta++)
+          trgradgp[j][theta]=gradgp[theta][j];
-     /* This loop fills the array Tvar from the string 'model'.*/
-     for(i=(j+1); i>=1;i--){
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+      for(i=1;i<=nlstate;i++)
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+        for(j=1;j<=nlstate;j++)
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+          vareij[i][j][(int)age] =0.;
-       /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /* Model includes a product */
+      for(h=0;h<=nhstepm;h++){
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+        for(k=0;k<=nhstepm;k++){
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-           cptcovprod--;
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-           cutv(strb,stre,strd,'V');
+          for(i=1;i<=nlstate;i++)
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+            for(j=1;j<=nlstate;j++)
-           cptcovage++;
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-             Tage[cptcovage]=i;
+        }
-             /*printf("stre=%s ", stre);*/
+      }
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+      /* pptj */
-           cptcovprod--;
+      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-           cutv(strb,stre,strc,'V');
+      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-           Tvar[i]=atoi(stre);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
-           cptcovage++;
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
-           Tage[cptcovage]=i;
+          varppt[j][i]=doldmp[j][i];
-         }
+      /* end ppptj */
-         else {  /* Age is not in the model */
+      /*  x centered again */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
+      if (popbased==1) {
-           Tvard[k1][1]=atoi(strc); /* m*/
+        if(mobilav ==0){
-           Tvard[k1][2]=atoi(stre); /* n */
+          for(i=1; i<=nlstate;i++)
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+            prlim[i][i]=probs[(int)age][i][ij];
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+        }else{ /* mobilav */
-           for (k=1; k<=lastobs;k++)
+          for(i=1; i<=nlstate;i++)
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+            prlim[i][i]=mobaverage[(int)age][i][ij];
-           k1++;
+        }
-           k2=k2+2;
+      }
-         }
-       }
+      /* This for computing probability of death (h=1 means
-       else { /* no more sum */
+         computed over hstepm (estepm) matrices product = hstepm*stepm months)
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+         as a weighted average of prlim.
-        /*  scanf("%d",i);*/
+      */
-       cutv(strd,strc,strb,'V');
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-       Tvar[i]=atoi(strc);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++){
-       }
+        for(i=1,gmp[j]=0.;i<= nlstate; i++)
-       strcpy(modelsav,stra);
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+      }
-         scanf("%d",i);*/
+      /* end probability of death */
-     } /* end of loop + */
-   } /* end model */
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-   /* 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);
+      fprintf(ficresprobmorprev,"\n");
-   scanf("%d ",i);*/
+      fprintf(ficresvij,"%.0f ",age );
+      for(i=1; i<=nlstate;i++)
-     /*  if(mle==1){*/
+        for(j=1; j<=nlstate;j++){
-   if (weightopt != 1) { /* Maximisation without weights*/
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-     for(i=1;i<=n;i++) weight[i]=1.0;
+        }
-   }
+      fprintf(ficresvij,"\n");
-     /*-calculation of age at interview from date of interview and age at death -*/
+      free_matrix(gp,0,nhstepm,1,nlstate);
-   agev=matrix(1,maxwav,1,imx);
+      free_matrix(gm,0,nhstepm,1,nlstate);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-   for (i=1; i<=imx; i++) {
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-     for(m=2; (m<= maxwav); m++) {
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+    } /* End age */
-         anint[m][i]=9999;
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
-         s[m][i]=-1;
+    free_vector(gmp,nlstate+1,nlstate+ndeath);
-       }
+    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-         nberr++;
+    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-         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(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
-         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);
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-         s[m][i]=-1;
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-       }
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-         nberr++;
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         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(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-       }
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-     }
+    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   }
+    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
-   for (i=1; i<=imx; i++)  {
+     */
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-     for(m=firstpass; (m<= lastpass); m++){
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-         if (s[m][i] >= nlstate+1) {
+    free_vector(xp,1,npar);
-           if(agedc[i]>0)
+    free_matrix(doldm,1,nlstate,1,nlstate);
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+    free_matrix(dnewm,1,nlstate,1,npar);
-               agev[m][i]=agedc[i];
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-             else {
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-               if ((int)andc[i]!=9999){
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-                 nbwarn++;
+    fclose(ficresprobmorprev);
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+    fflush(ficgp);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+    fflush(fichtm);
-                 agev[m][i]=-1;
+  }  /* end varevsij */
-               }
-             }
+ /************ Variance of prevlim ******************/
-         }
+  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+ {
-                                  years but with the precision of a month */
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-             agev[m][i]=1;
+   double **dnewm,**doldm;
-           else if(agev[m][i] <agemin){
+   int i, j, nhstepm, hstepm;
-             agemin=agev[m][i];
+   double *xp;
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+   double *gp, *gm;
-           }
+   double **gradg, **trgradg;
-           else if(agev[m][i] >agemax){
+   double **mgm, **mgp;
-             agemax=agev[m][i];
+   double age,agelim;
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   int theta;
-           }
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+   pstamp(ficresvpl);
-           /*     agev[m][i] = age[i]+2*m;*/
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-         }
+   fprintf(ficresvpl,"# Age");
-         else { /* =9 */
+   for(i=1; i<=nlstate;i++)
-           agev[m][i]=1;
+       fprintf(ficresvpl," %1d-%1d",i,i);
-           s[m][i]=-1;
+   fprintf(ficresvpl,"\n");
-         }
-       }
+   xp=vector(1,npar);
-       else /*= 0 Unknown */
+   dnewm=matrix(1,nlstate,1,npar);
-         agev[m][i]=1;
+   doldm=matrix(1,nlstate,1,nlstate);
-     }
+   hstepm=1*YEARM; /* Every year of age */
-   }
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   for (i=1; i<=imx; i++)  {
+   agelim = AGESUP;
-     for(m=firstpass; (m<=lastpass); m++){
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       if (s[m][i] > (nlstate+ndeath)) {
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nberr++;
+     if (stepm >= YEARM) hstepm=1;
-         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);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         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);
+     gradg=matrix(1,npar,1,nlstate);
-         goto end;
+     mgp=matrix(1,npar,1,nlstate);
-       }
+     mgm=matrix(1,npar,1,nlstate);
-     }
+     gp=vector(1,nlstate);
-   }
+     gm=vector(1,nlstate);
-   /*for (i=1; i<=imx; i++){
+     for(theta=1; theta <=npar; theta++){
-   for (m=firstpass; (m<lastpass); m++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
- }
+       }
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
- }*/
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+       for(i=1;i<=nlstate;i++){
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+         gp[i] = prlim[i][i];
+         mgp[theta][i] = prlim[i][i];
-   agegomp=(int)agemin;
+       }
-   free_vector(severity,1,maxwav);
+       for(i=1; i<=npar; i++) /* Computes gradient */
-   free_imatrix(outcome,1,maxwav+1,1,n);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   free_vector(moisnais,1,n);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-   free_vector(annais,1,n);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-   /* free_matrix(mint,1,maxwav,1,n);
+       else
-      free_matrix(anint,1,maxwav,1,n);*/
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-   free_vector(moisdc,1,n);
+       for(i=1;i<=nlstate;i++){
-   free_vector(andc,1,n);
+         gm[i] = prlim[i][i];
+         mgm[theta][i] = prlim[i][i];
+       }
-   wav=ivector(1,imx);
+       for(i=1;i<=nlstate;i++)
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+     } /* End theta */
-   /* Concatenates waves */
+     trgradg =matrix(1,nlstate,1,npar);
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+     for(j=1; j<=nlstate;j++)
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
-   Tcode=ivector(1,100);
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+     /*   printf("\nmgm mgp %d ",(int)age); */
-   ncodemax[1]=1;
+     /*   for(j=1; j<=nlstate;j++){ */
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
-                                  the estimations*/
+     /*  printf("\n "); */
-   h=0;
+     /*   } */
-   m=pow(2,cptcoveff);
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-   for(k=1;k<=cptcoveff; k++){
+     /*   printf("\n gradg %d ",(int)age); */
-     for(i=1; i <=(m/pow(2,k));i++){
+     /*   for(j=1; j<=nlstate;j++){ */
-       for(j=1; j <= ncodemax[k]; j++){
+     /*  printf("%d ",j); */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+     /*  for(theta=1; theta <=npar; theta++) */
-           h++;
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+     /*  printf("\n "); */
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+     /*   } */
-         }
+     /* } */
-       }
-     }
+     for(i=1;i<=nlstate;i++)
-   }
+       varpl[i][(int)age] =0.;
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-      codtab[1][2]=1;codtab[2][2]=2; */
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-   /* for(i=1; i <=m ;i++){
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-      for(k=1; k <=cptcovn; k++){
+     }else{
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-      }
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-      printf("\n");
+     }
-      }
+     for(i=1;i<=nlstate;i++)
-      scanf("%d",i);*/
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-   /*------------ gnuplot -------------*/
+     fprintf(ficresvpl,"%.0f ",age );
-   strcpy(optionfilegnuplot,optionfilefiname);
+     for(i=1; i<=nlstate;i++)
-   if(mle==-3)
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-     strcat(optionfilegnuplot,"-mort");
+     fprintf(ficresvpl,"\n");
-   strcat(optionfilegnuplot,".gp");
+     free_vector(gp,1,nlstate);
+     free_vector(gm,1,nlstate);
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     free_matrix(mgm,1,npar,1,nlstate);
-     printf("Problem with file %s",optionfilegnuplot);
+     free_matrix(mgp,1,npar,1,nlstate);
-   }
+     free_matrix(gradg,1,npar,1,nlstate);
-   else{
+     free_matrix(trgradg,1,nlstate,1,npar);
-     fprintf(ficgp,"\n# %s\n", version);
+   } /* End age */
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-     fprintf(ficgp,"set missing 'NaNq'\n");
+   free_vector(xp,1,npar);
-   }
+   free_matrix(doldm,1,nlstate,1,npar);
-   /*  fclose(ficgp);*/
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   /*--------- index.htm --------*/
+ }
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-   if(mle==-3)
+ /************ Variance of one-step probabilities  ******************/
-     strcat(optionfilehtm,"-mort");
+ 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[])
-   strcat(optionfilehtm,".htm");
+  {
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    int i, j=0,  k1, l1, tj;
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+    int k2, l2, j1,  z1;
-   }
+    int k=0, l;
+    int first=1, first1, first2;
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   strcat(optionfilehtmcov,"-cov.htm");
+    double **dnewm,**doldm;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+    double *xp;
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+    double *gp, *gm;
-   }
+    double **gradg, **trgradg;
-   else{
+    double **mu;
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+    double age, cov[NCOVMAX+1];
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+    int theta;
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+    char fileresprob[FILENAMELENGTH];
-   }
+    char fileresprobcov[FILENAMELENGTH];
+    char fileresprobcor[FILENAMELENGTH];
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+    double ***varpij;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+    strcpy(fileresprob,"PROB_");
- \n\
+    strcat(fileresprob,fileres);
- <hr  size=\"2\" color=\"#EC5E5E\">\
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-  <ul><li><h4>Parameter files</h4>\n\
+      printf("Problem with resultfile: %s\n", fileresprob);
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-  - 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\
+    strcpy(fileresprobcov,"PROBCOV_");
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+    strcat(fileresprobcov,fileresu);
-  - Date and time at start: %s</ul>\n",\
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-           fileres,fileres,\
+    }
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+    strcpy(fileresprobcor,"PROBCOR_");
-   fflush(fichtm);
+    strcat(fileresprobcor,fileresu);
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-   strcpy(pathr,path);
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-   strcat(pathr,optionfilefiname);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+    }
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-      and prints on file fileres'p'. */
+    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(fichtm,"\n");
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+    pstamp(ficresprob);
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+    fprintf(ficresprob,"# Age");
-           imx,agemin,agemax,jmin,jmax,jmean);
+    pstamp(ficresprobcov);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+    fprintf(ficresprobcov,"# Age");
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+    pstamp(ficresprobcor);
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+    fprintf(ficresprobcor,"# Age");
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+    for(i=1; i<=nlstate;i++)
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+      for(j=1; j<=(nlstate+ndeath);j++){
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
+      }
-   if (mle==-3){
+    /* fprintf(ficresprob,"\n");
-     ximort=matrix(1,NDIM,1,NDIM);
+       fprintf(ficresprobcov,"\n");
-     cens=ivector(1,n);
+       fprintf(ficresprobcor,"\n");
-     ageexmed=vector(1,n);
+    */
-     agecens=vector(1,n);
+    xp=vector(1,npar);
-     dcwave=ivector(1,n);
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-     for (i=1; i<=imx; i++){
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-       dcwave[i]=-1;
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-       for (m=firstpass; m<=lastpass; m++)
+    first=1;
-         if (s[m][i]>nlstate) {
+    fprintf(ficgp,"\n# Routine varprob");
-           dcwave[i]=m;
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+    fprintf(fichtm,"\n");
-           break;
-         }
+    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.</li>\n",optionfilehtmcov);
-     }
+    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
+    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-     for (i=1; i<=imx; i++) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-       if (wav[i]>0){
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-         ageexmed[i]=agev[mw[1][i]][i];
+    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. \
-         j=wav[i];
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-         agecens[i]=1.;
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ standard deviations wide on each axis. <br>\
-         if (ageexmed[i]> 1 && wav[i] > 0){
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-           agecens[i]=agev[mw[j][i]][i];
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-           cens[i]= 1;
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-         }else if (ageexmed[i]< 1)
-           cens[i]= -1;
+    cov[1]=1;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+    /* tj=cptcoveff; */
-           cens[i]=0 ;
+    tj = (int) pow(2,cptcoveff);
-       }
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-       else cens[i]=-1;
+    j1=0;
-     }
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
+      if  (cptcovn>0) {
-     for (i=1;i<=NDIM;i++) {
+        fprintf(ficresprob, "\n#********** Variable ");
-       for (j=1;j<=NDIM;j++)
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+        fprintf(ficresprob, "**********\n#\n");
-     }
+        fprintf(ficresprobcov, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     p[1]=0.0268; p[NDIM]=0.083;
+        fprintf(ficresprobcov, "**********\n#\n");
-     /*printf("%lf %lf", p[1], p[2]);*/
+        fprintf(ficgp, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+        fprintf(ficgp, "**********\n#\n");
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-       printf("Problem with resultfile: %s\n", filerespow);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-     }
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+        fprintf(ficresprobcor, "\n#********** Variable ");
-     /*  for (i=1;i<=nlstate;i++)
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for(j=1;j<=nlstate+ndeath;j++)
+        fprintf(ficresprobcor, "**********\n#");
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+        if(invalidvarcomb[j1]){
-     */
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-     fprintf(ficrespow,"\n");
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
+          continue;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+        }
-     fclose(ficrespow);
+      }
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
-     for(i=1; i <=NDIM; i++)
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-       for(j=i+1;j<=NDIM;j++)
+      for (age=bage; age<=fage; age ++){
-         matcov[i][j]=matcov[j][i];
+        cov[2]=age;
+        if(nagesqr==1)
-     printf("\nCovariance matrix\n ");
+          cov[3]= age*age;
-     for(i=1; i <=NDIM; i++) {
+        for (k=1; k<=cptcovn;k++) {
-       for(j=1;j<=NDIM;j++){
+          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-         printf("%f ",matcov[i][j]);
+          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-       }
+                                                                     * 1  1 1 1 1
-       printf("\n ");
+                                                                     * 2  2 1 1 1
-     }
+                                                                     * 3  1 2 1 1
+                                                                     */
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-     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]));
+        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-     lsurv=vector(1,AGESUP);
+        for (k=1; k<=cptcovprod;k++)
-     lpop=vector(1,AGESUP);
+          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-     tpop=vector(1,AGESUP);
-     lsurv[agegomp]=100000;
+        for(theta=1; theta <=npar; theta++){
-     for (k=agegomp;k<=AGESUP;k++) {
+          for(i=1; i<=npar; i++)
-       agemortsup=k;
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     }
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     for (k=agegomp;k<agemortsup;k++)
+          k=0;
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+          for(i=1; i<= (nlstate); i++){
+            for(j=1; j<=(nlstate+ndeath);j++){
-     for (k=agegomp;k<agemortsup;k++){
+              k=k+1;
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+              gp[k]=pmmij[i][j];
-       sumlpop=sumlpop+lpop[k];
+            }
-     }
+          }
-     tpop[agegomp]=sumlpop;
+          for(i=1; i<=npar; i++)
-     for (k=agegomp;k<(agemortsup-3);k++){
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-       /*  tpop[k+1]=2;*/
-       tpop[k+1]=tpop[k]-lpop[k];
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     }
+          k=0;
+          for(i=1; i<=(nlstate); i++){
+            for(j=1; j<=(nlstate+ndeath);j++){
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+              k=k+1;
-     for (k=agegomp;k<(agemortsup-2);k++)
+              gm[k]=pmmij[i][j];
-       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 / */
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+        }
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
-                      stepm, weightopt,\
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                      model,imx,p,matcov,agemortsup);
+          for(theta=1; theta <=npar; theta++)
+            trgradg[j][theta]=gradg[theta][j];
-     free_vector(lsurv,1,AGESUP);
-     free_vector(lpop,1,AGESUP);
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-     free_vector(tpop,1,AGESUP);
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-   } /* Endof if mle==-3 */
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
-   else{ /* For mle >=1 */
+        k=0;
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+        for(i=1; i<=(nlstate); i++){
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+          for(j=1; j<=(nlstate+ndeath);j++){
-     for (k=1; k<=npar;k++)
+            k=k+1;
-       printf(" %d %8.5f",k,p[k]);
+            mu[k][(int) age]=pmmij[i][j];
-     printf("\n");
+          }
-     globpr=1; /* to print the contributions */
+        }
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-     for (k=1; k<=npar;k++)
+            varpij[i][j][(int)age] = doldm[i][j];
-       printf(" %d %8.5f",k,p[k]);
-     printf("\n");
+        /*printf("\n%d ",(int)age);
-     if(mle>=1){ /* Could be 1 or 2 */
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+          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]));
+          }*/
-     /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+        fprintf(ficresprob,"\n%d ",(int)age);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-     for(i=1,jk=1; i <=nlstate; i++){
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       for(k=1; k <=(nlstate+ndeath); k++){
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-         if (k != i) {
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-           printf("%d%d ",i,k);
+        }
-           fprintf(ficlog,"%d%d ",i,k);
+        i=0;
-           fprintf(ficres,"%1d%1d ",i,k);
+        for (k=1; k<=(nlstate);k++){
-           for(j=1; j <=ncovmodel; j++){
+          for (l=1; l<=(nlstate+ndeath);l++){
-             printf("%lf ",p[jk]);
+            i++;
-             fprintf(ficlog,"%lf ",p[jk]);
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficres,"%lf ",p[jk]);
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-             jk++;
+            for (j=1; j<=i;j++){
-           }
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-           printf("\n");
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-           fprintf(ficlog,"\n");
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-           fprintf(ficres,"\n");
+            }
-         }
+          }
-       }
+        }/* end of loop for state */
-     }
+      } /* end of loop for age */
-     if(mle!=0){
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-       /* Computing hessian and covariance matrix */
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-       ftolhess=ftol; /* Usually correct */
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-     }
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+      /* Confidence intervalle of pij  */
-     printf("# Scales (for hessian or gradient estimation)\n");
+      /*
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+        fprintf(ficgp,"\nunset parametric;unset label");
-     for(i=1,jk=1; i <=nlstate; i++){
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-       for(j=1; j <=nlstate+ndeath; j++){
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         if (j!=i) {
+        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(ficres,"%1d%1d",i,j);
+        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-           printf("%1d%1d",i,j);
+        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-           fprintf(ficlog,"%1d%1d",i,j);
+        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-           for(k=1; k<=ncovmodel;k++){
+      */
-             printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-             fprintf(ficres," %.5e",delti[jk]);
+      first1=1;first2=2;
-             jk++;
+      for (k2=1; k2<=(nlstate);k2++){
-           }
+        for (l2=1; l2<=(nlstate+ndeath);l2++){
-           printf("\n");
+          if(l2==k2) continue;
-           fprintf(ficlog,"\n");
+          j=(k2-1)*(nlstate+ndeath)+l2;
-           fprintf(ficres,"\n");
+          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;
-     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");
+              for (age=bage; age<=fage; age ++){
-     if(mle>=1)
+                if ((int)age %5==0){
-       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");
+                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-     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");
+                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-     /* # 121 Var(a12)\n\ */
+                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                  mu1=mu[i][(int) age]/stepm*YEARM ;
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                  mu2=mu[j][(int) age]/stepm*YEARM;
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+                  c12=cv12/sqrt(v1*v2);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                  /* Computing eigen value of matrix of covariance */
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+                  if ((lc2 <0) || (lc1 <0) ){
+                    if(first2==1){
+                      first1=0;
-     /* Just to have a covariance matrix which will be more understandable
+                      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);
-        even is we still don't want to manage dictionary of variables
+                    }
-     */
+                    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);
-     for(itimes=1;itimes<=2;itimes++){
+                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
-       jj=0;
+                    /* lc2=fabs(lc2); */
-       for(i=1; i <=nlstate; i++){
+                  }
-         for(j=1; j <=nlstate+ndeath; j++){
-           if(j==i) continue;
+                  /* Eigen vectors */
-           for(k=1; k<=ncovmodel;k++){
+                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-             jj++;
+                  /*v21=sqrt(1.-v11*v11); *//* error */
-             ca[0]= k+'a'-1;ca[1]='\0';
+                  v21=(lc1-v1)/cv12*v11;
-             if(itimes==1){
+                  v12=-v21;
-               if(mle>=1)
+                  v22=v11;
-                 printf("#%1d%1d%d",i,j,k);
+                  tnalp=v21/v11;
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+                  if(first1==1){
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+                    first1=0;
-             }else{
+                    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);
-               if(mle>=1)
+                  }
-                 printf("%1d%1d%d",i,j,k);
+                  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);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+                  /*printf(fignu*/
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-             }
+                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-             ll=0;
+                  if(first==1){
-             for(li=1;li <=nlstate; li++){
+                    first=0;
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+                    fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
-                 if(lj==li) continue;
+                    fprintf(ficgp,"\nset parametric;unset label");
-                 for(lk=1;lk<=ncovmodel;lk++){
+                    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);
-                   ll++;
+                    fprintf(ficgp,"\nset ter svg size 640, 480");
-                   if(ll<=jj){
+                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
-                     if(ll<jj){
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
-                       if(itimes==1){
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
-                         if(mle>=1)
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                    fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                    fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                       }else{
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                         if(mle>=1)
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                           printf(" %.5e",matcov[jj][ll]);
+                    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",      \
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-                       }
+                  }else{
-                     }else{
+                    first=0;
-                       if(itimes==1){
+                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-                         if(mle>=1)
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,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", \
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
-                       }else{
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-                         if(mle>=1)
+                  }/* if first */
-                           printf(" %.5e",matcov[jj][ll]);
+                } /* age mod 5 */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+              } /* end loop age */
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+              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 */
-                 } /* end lk */
+        } /*l1 */
-               } /* end lj */
+      }/* k1 */
-             } /* end li */
+    }  /* loop on combination of covariates j1 */
-             if(mle>=1)
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-               printf("\n");
+    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-             fprintf(ficlog,"\n");
+    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-             fprintf(ficres,"\n");
+    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-             numlinepar++;
+    free_vector(xp,1,npar);
-           } /* end k*/
+    fclose(ficresprob);
-         } /*end j */
+    fclose(ficresprobcov);
-       } /* end i */
+    fclose(ficresprobcor);
-     } /* end itimes */
+    fflush(ficgp);
+    fflush(fichtmcov);
-     fflush(ficlog);
+  }
-     fflush(ficres);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ /******************* Printing html file ***********/
-       ungetc(c,ficpar);
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
-       fgets(line, MAXLINE, ficpar);
+                   int lastpass, int stepm, int weightopt, char model[],\
-       puts(line);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-       fputs(line,ficparo);
+                   int popforecast, int prevfcast, int backcast, int estepm , \
-     }
+                   double jprev1, double mprev1,double anprev1, double dateprev1, \
-     ungetc(c,ficpar);
+                   double jprev2, double mprev2,double anprev2, double dateprev2){
+   int jj1, k1, i1, cpt;
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-     if (fage <= 2) {
+ </ul>");
-       bage = ageminpar;
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
-       fage = agemaxpar;
+    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) ",
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+    fprintf(fichtm,"\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-     while((c=getc(ficpar))=='#' && c!= EOF){
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
-       ungetc(c,ficpar);
+    fprintf(fichtm,"\
-       fgets(line, MAXLINE, ficpar);
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-       puts(line);
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
-       fputs(line,ficparo);
+    fprintf(fichtm,"\
-     }
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-     ungetc(c,ficpar);
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
+    fprintf(fichtm,"\
-     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);
+  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-     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);
+            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
-     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(fichtm,"\
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+  - (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): \
-     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);
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
-     while((c=getc(ficpar))=='#' && c!= EOF){
+    if(prevfcast==1){
-       ungetc(c,ficpar);
+      fprintf(fichtm,"\
-       fgets(line, MAXLINE, ficpar);
+  - Prevalence projections by age and states:                            \
-       puts(line);
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
-       fputs(line,ficparo);
+    }
-     }
-     ungetc(c,ficpar);
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    m=pow(2,cptcoveff);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+    jj1=0;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+    for(k1=1; k1<=m;k1++){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+      jj1++;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      if (cptcovn > 0) {
-       ungetc(c,ficpar);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-       fgets(line, MAXLINE, ficpar);
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-       puts(line);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-       fputs(line,ficparo);
+          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
-     }
+        }
-     ungetc(c,ficpar);
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-     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);
+        if(invalidvarcomb[k1]){
-     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(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
-     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);
+          printf("\nCombination (%d) ignored because no cases \n",k1);
-     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);
+          continue;
-     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.*/
+      }
+      /* aij, bij */
+      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+ <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+      /* Pij */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+      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.svg\">%s_%d-2.svg</a><br> \
+ <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+      /* Quasi-incidences */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+      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, \
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+      /* Survival functions (period) in state j */
-    /*------------ free_vector  -------------*/
+      for(cpt=1; cpt<=nlstate;cpt++){
-    /*  chdir(path); */
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
-     free_ivector(wav,1,imx);
+      }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+      /* State specific survival functions (period) */
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+      for(cpt=1; cpt<=nlstate;cpt++){
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
-     free_lvector(num,1,n);
+  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
-     free_vector(agedc,1,n);
+  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+      }
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+      /* Period (stable) prevalence in each health state */
-     fclose(ficparo);
+      for(cpt=1; cpt<=nlstate;cpt++){
-     fclose(ficres);
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+      }
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+      if(backcast==1){
+        /* Period (stable) back prevalence in each health state */
-     strcpy(filerespl,"pl");
+        for(cpt=1; cpt<=nlstate;cpt++){
-     strcat(filerespl,fileres);
+          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+        }
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+      }
-     }
+      if(prevfcast==1){
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+        /* Projection of prevalence up to period (stable) prevalence in each health state */
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+        for(cpt=1; cpt<=nlstate;cpt++){
-     pstamp(ficrespl);
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+ <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
-     fprintf(ficrespl,"#Age ");
+        }
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+      }
-     fprintf(ficrespl,"\n");
+      for(cpt=1; cpt<=nlstate;cpt++) {
-     prlim=matrix(1,nlstate,1,nlstate);
+        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.svg\">%s_%d%d.svg</a> <br> \
+ <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
-     agebase=ageminpar;
+      }
-     agelim=agemaxpar;
+      /* } /\* end i1 *\/ */
-     ftolpl=1.e-10;
+    }/* End k1 */
-     i1=cptcoveff;
+    fprintf(fichtm,"</ul>");
-     if (cptcovn < 1){i1=1;}
+    fprintf(fichtm,"\
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
-         k=k+1;
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+ But because parameters are usually highly correlated (a higher incidence of disability \
-         fprintf(ficrespl,"\n#******");
+ and a higher incidence of recovery can give very close observed transition) it might \
-         printf("\n#******");
+ be very useful to look not only at linear confidence intervals estimated from the \
-         fprintf(ficlog,"\n#******");
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
-         for(j=1;j<=cptcoveff;j++) {
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ covariance matrix of the one-step probabilities. \
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
+    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-         fprintf(ficrespl,"******\n");
+            subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-         printf("******\n");
+    fprintf(fichtm,"\
-         fprintf(ficlog,"******\n");
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-         for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+    fprintf(fichtm,"\
-           fprintf(ficrespl,"%.0f ",age );
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-           for(j=1;j<=cptcoveff;j++)
+            subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    fprintf(fichtm,"\
-           for(i=1; i<=nlstate;i++)
+  - 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): \
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+    <a href=\"%s\">%s</a> <br>\n</li>",
-           fprintf(ficrespl,"\n");
+            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>",
-     fclose(ficrespl);
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
+    fprintf(fichtm,"\
-     /*------------- h Pij x at various ages ------------*/
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+    fprintf(fichtm,"\
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+  - 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",
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+    fprintf(fichtm,"\
-     }
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-     printf("Computing pij: result on file '%s' \n", filerespij);
+            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-     /*if (stepm<=24) stepsize=2;*/
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+ /*      <br>",fileres,fileres,fileres,fileres); */
-     agelim=AGESUP;
+ /*  else  */
-     hstepm=stepsize*YEARM; /* Every year of age */
+ /*    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); */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+    fflush(fichtm);
+    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
+    m=pow(2,cptcoveff);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+    jj1=0;
-         k=k+1;
+    for(k1=1; k1<=m;k1++){
-         fprintf(ficrespij,"\n#****** ");
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-         for(j=1;j<=cptcoveff;j++)
+      jj1++;
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      if (cptcovn > 0) {
-         fprintf(ficrespij,"******\n");
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+        if(invalidvarcomb[k1]){
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
-           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(cpt=1; cpt<=nlstate;cpt++) {
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
-           for(i=1; i<=nlstate;i++)
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
-             for(j=1; j<=nlstate+ndeath;j++)
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
-               fprintf(ficrespij," %1d-%1d",i,j);
+      }
-           fprintf(ficrespij,"\n");
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-           for (h=0; h<=nhstepm; h++){
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+ true period expectancies (those weighted with period prevalences are also\
-             for(i=1; i<=nlstate;i++)
+  drawn in addition to the population based expectancies computed using\
-               for(j=1; j<=nlstate+ndeath;j++)
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-             fprintf(ficrespij,"\n");
+      /* } /\* end i1 *\/ */
-           }
+    }/* End k1 */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    fprintf(fichtm,"</ul>");
-           fprintf(ficrespij,"\n");
+    fflush(fichtm);
-         }
+ }
-       }
-     }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   char dirfileres[132],optfileres[132];
-     fclose(ficrespij);
+   char gplotcondition[132];
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   int lv=0, vlv=0, kl=0;
-     for(i=1;i<=AGESUP;i++)
+   int ng=0;
-       for(j=1;j<=NCOVMAX;j++)
+   int vpopbased;
-         for(k=1;k<=NCOVMAX;k++)
+   int ioffset; /* variable offset for columns */
-           probs[i][j][k]=0.;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     /*---------- Forecasting ------------------*/
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     if(prevfcast==1){
+ /*   } */
-       /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+   /*#ifdef windows */
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-       /*      }  */
+   /*#endif */
-       /*      else{ */
+   m=pow(2,cptcoveff);
-       /*        erreur=108; */
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+   /* Contribution to likelihood */
-       /*        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); */
+   /* 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");
-     /*---------- Health expectancies and variances ------------*/
+ /* 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 */
-     strcpy(filerest,"t");
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
-     strcat(filerest,fileres);
+   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+   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(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   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));
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   for (i=1; i<= nlstate ; i ++) {
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     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);
-     strcpy(filerese,"e");
+     for (j=2; j<= nlstate+ndeath ; j ++) {
-     strcat(filerese,fileres);
+       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);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+     }
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     fprintf(ficgp,";\nset out; unset ylabel;\n");
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   }
-     }
+   /* 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 */
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   /* 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");
-     strcpy(fileresstde,"stde");
+   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
-     strcat(fileresstde,fileres);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   strcpy(dirfileres,optionfilefiname);
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   strcpy(optfileres,"vpl");
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   /* 1eme*/
-     }
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
-     strcpy(filerescve,"cve");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-     strcat(filerescve,fileres);
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+         /* 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 */
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
-     strcpy(fileresv,"v");
+       fprintf(ficgp,"\n#\n");
-     strcat(fileresv,fileres);
+       if(invalidvarcomb[k1]){
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+         continue;
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+       }
-     }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \n\
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+ set ylabel \"Probability\" \n   \
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ set ter svg size 640, 480\n     \
-     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
+       for (i=1; i<= nlstate ; i ++) {
+         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     if (mobilav!=0) {
+         else        fprintf(ficgp," %%*lf (%%*lf)");
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       }
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       for (i=1; i<= nlstate ; i ++) {
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         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:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for (i=1; i<= nlstate ; i ++) {
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         k=k+1;
+         else fprintf(ficgp," %%*lf (%%*lf)");
-         fprintf(ficrest,"\n#****** ");
+       }
-         for(j=1;j<=cptcoveff;j++)
+       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
-         fprintf(ficrest,"******\n");
+         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
-         fprintf(ficreseij,"\n#****** ");
+         if(cptcoveff ==0){
-         fprintf(ficresstdeij,"\n#****** ");
+           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
-         fprintf(ficrescveij,"\n#****** ");
+         }else{
-         for(j=1;j<=cptcoveff;j++) {
+           kl=0;
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             /* 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 */
-         fprintf(ficreseij,"******\n");
+             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         fprintf(ficresstdeij,"******\n");
+             vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficrescveij,"******\n");
+             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 *\/ */
-         fprintf(ficresvij,"\n#****** ");
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
-         for(j=1;j<=cptcoveff;j++)
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
-         fprintf(ficresvij,"******\n");
+             if(k==cptcoveff){
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
++(cpt-1),  cpt );  /* 4 or 6 ?*/
-         oldm=oldms;savm=savms;
+             }else{
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+               kl++;
+             }
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+           } /* end covariate */
-         oldm=oldms;savm=savms;
+         } /* end if no covariate */
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+       } /* end if backcast */
-         if(popbased==1){
+       fprintf(ficgp,"\nset out \n");
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+     } /* k1 */
-         }
+   } /* cpt */
+   /*2 eme*/
-         pstamp(ficrest);
+   for (k1=1; k1<= m ; k1 ++) {
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-         fprintf(ficrest,"\n");
+     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 */
-         epj=vector(1,nlstate+1);
+       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         for(age=bage; age <=fage ;age++){
+       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           if (popbased==1) {
+       vlv= nbcode[Tvaraff[k]][lv];
-             if(mobilav ==0){
+       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-               for(i=1; i<=nlstate;i++)
+     }
-                 prlim[i][i]=probs[(int)age][i][k];
+     fprintf(ficgp,"\n#\n");
-             }else{ /* mobilav */
+     if(invalidvarcomb[k1]){
-               for(i=1; i<=nlstate;i++)
+       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+       continue;
-             }
+     }
-           }
+     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-           fprintf(ficrest," %4.0f",age);
+     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+       if(vpopbased==0)
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+       else
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+         fprintf(ficgp,"\nreplot ");
-             }
+       for (i=1; i<= nlstate+1 ; i ++) {
-             epj[nlstate+1] +=epj[j];
+         k=2*i;
-           }
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
-           for(i=1, vepp=0.;i <=nlstate;i++)
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-             for(j=1;j <=nlstate;j++)
+           else fprintf(ficgp," %%*lf (%%*lf)");
-               vepp += vareij[i][j][(int)age];
+         }
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-           for(j=1;j <=nlstate;j++){
+         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-           }
+         for (j=1; j<= nlstate+1 ; j ++) {
-           fprintf(ficrest,"\n");
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-         }
+           else fprintf(ficgp," %%*lf (%%*lf)");
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         }
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         free_vector(epj,1,nlstate+1);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-       }
+         for (j=1; j<= nlstate+1 ; j ++) {
-     }
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-     free_vector(weight,1,n);
+           else fprintf(ficgp," %%*lf (%%*lf)");
-     free_imatrix(Tvard,1,15,1,2);
+         }
-     free_imatrix(s,1,maxwav+1,1,n);
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-     free_matrix(anint,1,maxwav,1,n);
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-     free_matrix(mint,1,maxwav,1,n);
+       } /* state */
-     free_ivector(cod,1,n);
+     } /* vpopbased */
-     free_ivector(tab,1,NCOVMAX);
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-     fclose(ficreseij);
+   } /* k1 */
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
-     fclose(ficresvij);
+   /*3eme*/
-     fclose(ficrest);
+   for (k1=1; k1<= m ; k1 ++) {
-     fclose(ficpar);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-     /*------- Variance of period (stable) prevalence------*/
+       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     strcpy(fileresvpl,"vpl");
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-     strcat(fileresvpl,fileres);
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       exit(0);
+         vlv= nbcode[Tvaraff[k]][lv];
-     }
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+       }
+       fprintf(ficgp,"\n#\n");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       if(invalidvarcomb[k1]){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         k=k+1;
+         continue;
-         fprintf(ficresvpl,"\n#****** ");
+       }
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       /*       k=2+nlstate*(2*cpt-2); */
-         fprintf(ficresvpl,"******\n");
+       k=2+(nlstate+1)*(cpt-1);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       fprintf(ficgp,"set ter svg size 640, 480\n\
-         oldm=oldms;savm=savms;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-       }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     }
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-     fclose(ficresvpl);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     /*---------- End : free ----------------*/
+       */
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for (i=1; i< nlstate ; i ++) {
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"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);*/
-   }  /* mle==-3 arrives here for freeing */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+       }
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     }
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   }
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   /* 4eme */
-     free_matrix(matcov,1,npar,1,npar);
+   /* Survival functions (period) from state i in state j by initial state i */
-     /*free_vector(delti,1,npar);*/
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_matrix(agev,1,maxwav,1,imx);
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       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 */
-     free_ivector(ncodemax,1,8);
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-     free_ivector(Tvar,1,15);
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-     free_ivector(Tprod,1,15);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     free_ivector(Tvaraff,1,15);
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     free_ivector(Tage,1,15);
+         vlv= nbcode[Tvaraff[k]][lv];
-     free_ivector(Tcode,1,100);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+       fprintf(ficgp,"\n#\n");
-     free_imatrix(codtab,1,100,1,10);
+       if(invalidvarcomb[k1]){
-   fflush(fichtm);
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   fflush(ficgp);
+         continue;
+       }
-   if((nberr >0) || (nbwarn>0)){
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+ set ter svg size 640, 480\n                                                                                                                                                                                     \
-   }else{
+ unset log y\n                                                                                                                                                                                                                                           \
-     printf("End of Imach\n");
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     fprintf(ficlog,"End of Imach\n");
+       k=3;
-   }
+       for (i=1; i<= nlstate ; i ++){
-   printf("See log file on %s\n",filelog);
+         if(i==1){
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-   (void) gettimeofday(&end_time,&tzp);
+         }else{
-   tm = *localtime(&end_time.tv_sec);
+           fprintf(ficgp,", '' ");
-   tmg = *gmtime(&end_time.tv_sec);
+         }
-   strcpy(strtend,asctime(&tm));
+         l=(nlstate+ndeath)*(i-1)+1;
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+         for (j=2; j<= nlstate+ndeath ; j ++)
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+       } /* nlstate */
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+       fprintf(ficgp,"\nset out\n");
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     } /* end cpt state*/
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+   } /* end covariate */
- /*   if(fileappend(fichtm,optionfilehtm)){ */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+ /* 5eme */
-   fclose(fichtm);
+   /* Survival functions (period) from state i in state j by final state j */
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
-   fclose(fichtmcov);
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
-   fclose(ficgp);
-   fclose(ficlog);
+       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);
-   /*------ End -----------*/
+       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 */
-    printf("Before Current directory %s!\n",pathcd);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-    if(chdir(pathcd) != 0)
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     printf("Can't move to directory %s!\n",path);
+         vlv= nbcode[Tvaraff[k]][lv];
-   if(getcwd(pathcd,MAXLINE) > 0)
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     printf("Current directory %s!\n",pathcd);
+       }
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+       fprintf(ficgp,"\n#\n");
-   sprintf(plotcmd,"gnuplot");
+       if(invalidvarcomb[k1]){
- #ifndef UNIX
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+         continue;
- #endif
+       }
-   if(!stat(plotcmd,&info)){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ set ter svg size 640, 480\n                                             \
-     }else
+ unset log y\n                                                           \
-       strcpy(pplotcmd,plotcmd);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
- #ifdef UNIX
+       k=3;
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-     if(!stat(plotcmd,&info)){
+         if(j==1)
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-     }else
+         else
-       strcpy(pplotcmd,plotcmd);
+           fprintf(ficgp,", '' ");
- #endif
+         l=(nlstate+ndeath)*(cpt-1) +j;
-   }else
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-     strcpy(pplotcmd,plotcmd);
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+       } /* nlstate */
+       fprintf(ficgp,", '' ");
-   if((outcmd=system(plotcmd)) != 0){
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-     printf("\n Problem with gnuplot\n");
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-   }
+         l=(nlstate+ndeath)*(cpt-1) +j;
-   printf(" Wait...");
+         if(j < nlstate)
-   while (z[0] != 'q') {
+           fprintf(ficgp,"$%d +",k+l);
-     /* chdir(path); */
+         else
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-     scanf("%s",z);
+       }
- /*     if (z[0] == 'c') system("./imach"); */
+       fprintf(ficgp,"\nset out\n");
-     if (z[0] == 'e') {
+     } /* end cpt state*/
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+   } /* end covariate */
-       system(optionfilehtm);
-     }
+ /* 6eme */
-     else if (z[0] == 'g') system(plotcmd);
+   /* CV preval stable (period) for each covariate */
-     else if (z[0] == 'q') exit(0);
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
-   }
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-   end:
-   while (z[0] != 'q') {
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
-     printf("\nType  q for exiting: ");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     scanf("%s",z);
+         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);
+       }
+       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,"P_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3; /* Offset */
+       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/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+ /* 7eme */
+   if(backcast == 1){
+     /* CV back preval stable (period) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): '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);
+         }
+         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,"PB_"),cpt,k1);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3; /* Offset */
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+           else
+             fprintf(ficgp,", '' ");
+           /* l=(nlstate+ndeath)*(i-1)+1; */
+           l=(nlstate+ndeath)*(cpt-1)+1;
+           /* 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+(cpt-1)+i-1); /* a vérifier */
+           /* 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",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
+   /* 8eme */
+   if(prevfcast==1){
+     /* Projection from cross-sectional to stable (period) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (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);
+         }
+         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.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         for (i=1; 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==1){
+             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)) t 'pw.%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             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 */
+             if(cptcoveff ==1){
+               ioffset=4; /* Age is in 4 */
+             }else{
+               ioffset=6; /* Age is in 6 */
+               /*#  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 */
+             }
+             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) t 'p.%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             }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\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevfcast */
+   /* proba elementaires */
+   fprintf(ficgp,"\n##############\n#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;*/
+   fprintf(ficgp,"\n##############\n#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,"# ng=%d\n",ng);
+     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+     for(jk=1; jk <=m; jk++) {
+       fprintf(ficgp,"#    jk=%d\n",jk);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+       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 */
+             for(j=3; j <=ncovmodel-nagesqr; j++) {
+               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+               if(ij <=cptcovage) { /* Bug valgrind */
+                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   ij++;
+                 }
+               }
+               else
+                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
+             }
+           }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(k1=1; k1 <=nlstate; k1++){
+               if(nagesqr==0)
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+               ij=1;
+               for(j=3; j <=ncovmodel-nagesqr; j++){
+                 if(ij <=cptcovage) { /* Bug valgrind */
+                   if((j-2)==Tage[ij]) { /* Bug valgrind */
+                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                     ij++;
+                   }
+                 }
+                 else
+                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
+               }
+               fprintf(ficgp,")");
+             }
+             fprintf(ficgp,")");
+             if(ng ==2)
+               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+             else /* ng= 3 */
+               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+           }else{ /* end ng <> 1 */
+             if( k !=k2) /* logit p11 is hard to draw */
+               fprintf(ficgp," t \"logit(p%d%d)\" ", 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\n");
+     } /* end jk */
+   } /* 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;
+    double sum=0.;
+    double age;
+    double *sumnewp, *sumnewm;
+    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
+    /* 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);
+    agemingood = vector(1,ncovcombmax);
+    agemaxgood = vector(1,ncovcombmax);
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      sumnewm[cptcod]=0.;
+      sumnewp[cptcod]=0.;
+      agemingood[cptcod]=0;
+      agemaxgood[cptcod]=0;
+    }
+    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
+    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+      if(mobilav==1) mobilavrange=5; /* default */
+      else mobilavrange=mobilav;
+      for (age=bage; age<=fage; age++)
+        for (i=1; i<=nlstate;i++)
+          for (cptcod=1;cptcod<=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 (i=1; i<=nlstate;i++){
+            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+              for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+              }
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+            }
+          }
+        }/* end age */
+      }/* end mob */
+    }else
+      return -1;
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      /* 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;
+      }
+      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        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 */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+      /* From youngest, finding the oldest wrong */
+      agemaxgood[cptcod]=bage+(mob-1)/2;
+      for (age=bage+(mob-1)/2; age<=fage; age++){
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemaxgood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      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(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
+    free_vector(agemaxgood,1, ncovcombmax);
+    free_vector(agemingood,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 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;
+   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("Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   fprintf(ficlog,"Computing 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;
+   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(k=1;k<=i1;k++){
+     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)]);
+     }
+     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--){
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==yearp) {
+             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]*mobaverage[(int)agec][i][k];
+               else {
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+               }
+               if (h*hstepm/YEARM*stepm== yearp) {
+                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+               }
+             } /* end i */
+             if (h*hstepm/YEARM*stepm==yearp) {
+               fprintf(ficresf," %.3f", ppij);
+             }
+           }/* end j */
+         } /* end h */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+     } /* end yearp */
+   } /* end  k */
+   fclose(ficresf);
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
+ }
+ /* /\************** Back Forecasting ******************\/ */
+ /* void prevbackforecast(char fileres[], 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 en of backection (same day and month as back1). */
+ /*   *\/ */
+ /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
+ /*   double agec; /\* generic age *\/ */
+ /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
+ /*   double *popeffectif,*popcount; */
+ /*   double ***p3mat; */
+ /*   /\* double ***mobaverage; *\/ */
+ /*   char fileresfb[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); *\/ */
+ /*   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("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+ /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
+ /*   /\* if (mobilav!=0) { *\/ */
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+ /*   /\*   } *\/ */
+ /*   /\* } *\/ */
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
+ /*   if (stepm<=12) stepsize=1; */
+ /*   if(estepm < stepm){ */
+ /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
+ /*   } */
+ /*   else  hstepm=estepm;    */
+ /*   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=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);  */
+ /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+ /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+ /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
+ /*       k=k+1; */
+ /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.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)]); */
+ /*       } */
+ /*       fprintf(ficresfb," yearbproj age"); */
+ /*       for(j=1; j<=nlstate+ndeath;j++){  */
+ /*                              for(i=1; i<=nlstate;i++)               */
+ /*           fprintf(ficresfb," p%d%d",i,j); */
+ /*                              fprintf(ficresfb," p.%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);    */
+ /*                              for (agec=fage; agec>=(ageminpar-1); 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; */
+ /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
+ /*                                      for (h=0; h<=nhstepm; h++){ */
+ /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
+ /*               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(j=1; j<=nlstate+ndeath;j++) { */
+ /*                                                      ppij=0.; */
+ /*                                                      for(i=1; i<=nlstate;i++) { */
+ /*                                                              if (mobilav==1)  */
+ /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
+ /*                                                              else { */
+ /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
+ /*                                                              } */
+ /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
+ /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
+ /*                                                              } */
+ /*                                                      } /\* end i *\/ */
+ /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
+ /*                                                              fprintf(ficresfb," %.3f", ppij); */
+ /*                                                      } */
+ /*                                              }/\* end j *\/ */
+ /*                                      } /\* end h *\/ */
+ /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*                              } /\* end agec *\/ */
+ /*       } /\* end yearp *\/ */
+ /*     } /\* end cptcod *\/ */
+ /*   } /\* end  cptcov *\/ */
+ /*   /\* if (mobilav!=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"); */
+ /* } */
+ /************** 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;
+   int lstra;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[MAXLINE], strb[MAXLINE];
+   char *stratrunc;
+   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 removespace(char **stri){/*, char stro[]) {*/
+   char *p1 = *stri, *p2 = *stri;
+   do
+     while (*p2 == ' ')
+       p2++;
+   while (*p1++ == *p2++);
+   *stri=p1;
+ }
+ int decoderesult ( char resultline[])
+ /**< This routine decode one result line and returns the combination # of dummy covariates only **/
+ {
+   int j=0, k=0;
+   char resultsav[MAXLINE];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   removespace(&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'=' */
+   }
+   for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
+     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 */
+     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 */
+   }
+   return (0);
+ }
+ int selected( int kvar){ /* Selected combination of covariates */
+   if(Tvarsel[kvar])
+     return (0);
+   else
+     return(1);
+ }
+ 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;
+   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, ncovf=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 || Typevar[k]==2)){ /* Simple or product 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;
+       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){
+       Fixed[k]= 1;
+       Dummy[k]= 0;
+       ntveff++; /* Only simple time varying dummy variable */
+                         modell[k].maintype= VTYPE;
+                         modell[k].subtype= VD;
+                         ncovv++; /* Only simple time varying variables */
+                         TvarV[ncovv]=Tvar[k];
+                         TvarVind[ncovv]=k;
+       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 */
+                         TvarV[ncovv]=Tvar[k];
+                         TvarVind[ncovv]=k;
+       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];
+                         ncovv++; /* Only time varying variables */
+                         TvarV[ncovv]=Tvar[k];
+                         TvarVind[ncovv]=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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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] == 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[Tvar[k1]],Dummy[Tvar[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[Tvar[k1]],Dummy[Tvar[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\n",ncovf,ncovv,ncova);
+   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d\n",ncovf,ncovv,ncova);
+   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 )
+ {
+   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("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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         }
+         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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         (*nberr)++;
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
+       if(s[m][i] >0  || s[m][i]==-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 "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
+ #include <stdint.h>
+    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  (period or stable prevalence) --------------*/
+   int i, j, k, i1 ;
+   /* 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 period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# 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 dummy covariates */
+   if (cptcovn < 1){i1=1;}
+   for(k=1; k<=i1;k++){
+   /* 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)]);
+     }
+     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);
+       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 */
+   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  (period or 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 ;
+   /* 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 period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+   }
+   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   pstamp(ficresplb);
+   fprintf(ficresplb,"# Period (stable) back 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(k=1; k<=i1;k++){
+     //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)]);
+     }
+     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);
+       }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);
+       }
+       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 */
+   } /* cptcov */
+   /* 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;
+   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 (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*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;
+   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=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 Pij x Back Probability to be in state i at age x-h being in j 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 (k=1; k <= (int) pow(2,cptcoveff); k++){
+     fprintf(ficrespijb,"\n#****** ");
+     for(j=1;j<=cptcoveff;j++)
+       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     fprintf(ficrespijb,"******\n");
+     if(invalidvarcomb[k]){
+       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);
+       /* 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);
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+       fprintf(ficrespijb,"# Cov Agex agex-h hpijx 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");
+     }
+     /*}*/
+   }
+   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, 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;
+   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 model[MAXLINE], modeltemp[MAXLINE];
+   char resultline[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10;
+   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;
+   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  *p;
+   double **matcov; /* Matrix of covariance */
+   double **hess; /* Hessian matrix */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
+   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{
+     strcpy(pathtot,argv[1]);
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   /*cygwin_split_path(pathtot,path,optionfile);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #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;
+   }
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
+     /* First parameter line */
+   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,"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");
+     }
+     numlinepar++;
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+   }
+   /* Second parameter line */
+   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,"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);
+     }
+     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);
+   }
+   /* 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++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled == 0)
+             model[0]='\0';
+     else 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);
+   }
+   /* 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 with '.' \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 file.\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,1,n);  /**< used in readdata */
+   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */
+   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
+   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 */
+     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);
+     for(i=1; i <=nlstate; i++){
+                         j=0;
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+                                 if(jj==i) continue;
+                                 j++;
+                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+                                 if ((i1 != i) || (j1 != 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 scales values */
+     p=param[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+                                 if ( (i1-i) * (j1-j) != 0){
+                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+                                         exit(1);
+                                 }
+                                 printf("%1d%1d",i,j);
+                                 fprintf(ficparo,"%1d%1d",i1,j1);
+                                 fprintf(ficlog,"%1d%1d",i1,j1);
+                                 for(k=1; k<=ncovmodel;k++){
+                                         fscanf(ficpar,"%le",&delti3[i][j][k]);
+                                         printf(" %le",delti3[i][j][k]);
+                                         fprintf(ficparo," %le",delti3[i][j][k]);
+                                         fprintf(ficlog," %le",delti3[i][j][k]);
+                                 }
+                                 fscanf(ficpar,"\n");
+                                 numlinepar++;
+                                 printf("\n");
+                                 fprintf(ficparo,"\n");
+                                 fprintf(ficlog,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads covariance matrix */
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     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);
+     /*-------- 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;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
+   /*  Main data
+    */
+   n= 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[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,1,n);
+   anint=matrix(1,maxwav,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   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. */
+   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); /*  */
+   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,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   /* free_vector(moisdc,1,n); */
+   /* free_vector(andc,1,n); */
+   /* */
+   wav=ivector(1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   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);
+   /* */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* 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, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+               firstpass, lastpass,  stepm,  weightopt, model);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ 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(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     /*printf("%lf %lf", p[1], p[2]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #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(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+ #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 */
+       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((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     printf("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){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficlog,"pop_based=%d\n",popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     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);
+     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.*/
+     /* Results */
+     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((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+       if (num_filled == 0)
+         resultline[0]='\0';
+       else if (num_filled != 1){
+         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
+       }
+       printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
+       decoderesult(resultline);
+       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 (feof(ficpar))
+         break;
+       else{ /* Processess output results for this combination of covariate values */
+       }
+     }
+     /* 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);
+     }
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+     /*------------ 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,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /* 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 covariates in probs[age][status][cov] */
+     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     for(i=1;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(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       for(i=1;i<=AGESUP;i++)
+         for(j=1;j<=nlstate;j++)
+           for(k=1;k<=ncovcombmax;k++)
+             mobaverages[i][j][k]=0.;
+       mobaverage=mobaverages;
+       if (mobilav!=0) {
+         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);
+         }
+       }
+       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+       else if (mobilavproj !=0) {
+         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);
+         }
+       }
+     }/* end if moving average */
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+     }
+     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);
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
+       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       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);
+     }
+     /* ------ 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);
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
+       fprintf(ficreseij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       fprintf(ficreseij,"******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     }
+     fclose(ficreseij);
+     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);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       printf("\n#****** ");
+       fprintf(ficrest,"\n#****** ");
+       fprintf(ficlog,"\n#****** ");
+       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)]);
+       }
+       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)]);
+       }
+       fprintf(ficresstdeij,"******\n");
+       fprintf(ficrescveij,"******\n");
+       fprintf(ficresvij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresvij,"******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       printf(" cvevsij combination#=%d, ",k);
+       fprintf(ficlog, " cvevsij combination#=%d, ",k);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       printf(" end cvevsij \n ");
+       fprintf(ficlog, " end cvevsij \n ");
+       /*
+        */
+       /* goto endfree; */
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       pstamp(ficrest);
+       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); /* 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 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"); */
+         epj=vector(1,nlstate+1);
+         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*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_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_vector(epj,1,nlstate+1);
+       printf("done \n");fflush(stdout);
+       fprintf(ficlog,"done\n");fflush(ficlog);
+       /*}*/
+     } /* End k */
+     printf("done State-specific expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(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)]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     printf("done variance-covariance of period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0 ||mobilavproj !=0)
+       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+     free_ma3x(probs,1,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);
+   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+   free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
+   free_matrix(coqvar,1,maxwav,1,n);
+   free_matrix(covar,0,NCOVMAX,1,n);
+   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(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(Typevar,-1,NCOVMAX);
+   free_ivector(Tvar,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 -----------*/
+   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);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("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);
+   }
+   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);
+   }
+ }

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