imach/src/imach.c - diff

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Diff for /imach/src/imach.c between versions 1.125 and 1.220

-version 1.125, 2006/04/04 15:20:31
+version 1.220, 2016/02/15 23:22:02
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.220  2016/02/15 23:22:02  brouard
+   Summary: 0.99r2
+   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
    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    first survey ("cross") where individuals from different ages are
    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
    second wave of interviews ("longitudinal") which measure each change
    (if any) in individual health status.  Health expectancies are
    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
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
    probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
    complex model than "constant and age", you should modify the program
    where the markup *Covariates have to be included here again* invites
    you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
    multinomial logistic model, is clear when the delay between waves is not
    identical for each individual. Also, if a individual missed an
    intermediate interview, the information is lost, but taken into
    account using an interpolation or extrapolation.
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
    states. This elementary transition (by month, quarter,
    semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+ Back prevalence and projections:
-            Institut national d'�tudes d�mographiques, Paris.
+  - 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)
-   This software have been partly granted by Euro-REVES, a concerted action
+     Computes the back prevalence limit  for any combination     of covariate values k
-   from the European Union.
+     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
-   It is copyrighted identically to a GNU software product, ie programme and
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
-   software can be distributed freely for non commercial use. Latest version
+  - hBijx Back Probability to be in state i at age x-h being in j at x
-   can be accessed at http://euroreves.ined.fr/imach .
+    Computes for any combination of covariates k and any age between bage and fage
+    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
+                         oldm=oldms;savm=savms;
-   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
+          - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+      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
-   main
+      nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
-   read parameterfile
+      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
-   read datafile
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-   concatwav
-   freqsummary
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-   if (mle >= 1)
+            Institut national d'études démographiques, Paris.
-     mlikeli
+   This software have been partly granted by Euro-REVES, a concerted action
-   print results files
+   from the European Union.
-   if mle==1
+   It is copyrighted identically to a GNU software product, ie programme and
-      computes hessian
+   software can be distributed freely for non commercial use. Latest version
-   read end of parameter file: agemin, agemax, bage, fage, estepm
+   can be accessed at http://euroreves.ined.fr/imach .
-       begin-prev-date,...
-   open gnuplot file
+   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
-   open html file
+   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
-   period (stable) prevalence
-    for age prevalim()
+   **********************************************************************/
-   h Pij x
+ /*
-   variance of p varprob
+   main
-   forecasting if prevfcast==1 prevforecast call prevalence()
+   read parameterfile
-   health expectancies
+   read datafile
-   Variance-covariance of DFLE
+   concatwav
-   prevalence()
+   freqsummary
-    movingaverage()
+   if (mle >= 1)
-   varevsij()
+     mlikeli
-   if popbased==1 varevsij(,popbased)
+   print results files
-   total life expectancies
+   if mle==1
-   Variance of period (stable) prevalence
+      computes hessian
-  end
+   read end of parameter file: agemin, agemax, bage, fage, estepm
- */
+       begin-prev-date,...
+   open gnuplot file
+   open html file
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
- #include <math.h>
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
- #include <stdio.h>
+     freexexit2 possible for memory heap.
- #include <stdlib.h>
- #include <string.h>
+   h Pij x                         | pij_nom  ficrestpij
- #include <unistd.h>
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
- #include <limits.h>
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
- #include <sys/types.h>
- #include <sys/stat.h>
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
- #include <errno.h>
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
- extern int errno;
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- /* #include <sys/time.h> */
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
- #include <time.h>
- #include "timeval.h"
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
- /* #include <libintl.h> */
+   Variance-covariance of DFLE
- /* #define _(String) gettext (String) */
+   prevalence()
+    movingaverage()
- #define MAXLINE 256
+   varevsij()
+   if popbased==1 varevsij(,popbased)
- #define GNUPLOTPROGRAM "gnuplot"
+   total life expectancies
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+   Variance of period (stable) prevalence
- #define FILENAMELENGTH 132
+  end
+ */
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ /* #define DEBUG */
+ /* #define DEBUGBRENT */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ /* #define DEBUGLINMIN */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ /* #define DEBUGHESS */
+ #define DEBUGHESSIJ
- #define NINTERVMAX 8
+ #define LINMINORIGINAL  /* Don't use loop on scale in linmin (accepting nan)*/
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #define POWELL /* Instead of NLOPT */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #define POWELLF1F3 /* Skip test */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
- #define MAXN 20000
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
- #define YEARM 12. /* Number of months per year */
- #define AGESUP 130
+ #include <math.h>
- #define AGEBASE 40
+ #include <stdio.h>
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #include <stdlib.h>
- #ifdef UNIX
+ #include <string.h>
- #define DIRSEPARATOR '/'
- #define CHARSEPARATOR "/"
+ #ifdef _WIN32
- #define ODIRSEPARATOR '\\'
+ #include <io.h>
- #else
+ #include <windows.h>
- #define DIRSEPARATOR '\\'
+ #include <tchar.h>
- #define CHARSEPARATOR "\\"
+ #else
- #define ODIRSEPARATOR '/'
+ #include <unistd.h>
  #endif
- /* $Id$ */
+ #include <limits.h>
- /* $State$ */
+ #include <sys/types.h>
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #if defined(__GNUC__)
- char fullversion[]="$Revision$ $Date$";
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- char strstart[80];
+ #endif
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ #include <sys/stat.h>
- int nvar;
+ #include <errno.h>
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ /* extern int errno; */
- int npar=NPARMAX;
- int nlstate=2; /* Number of live states */
+ /* #ifdef LINUX */
- int ndeath=1; /* Number of dead states */
+ /* #include <time.h> */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ /* #include "timeval.h" */
- int popbased=0;
+ /* #else */
+ /* #include <sys/time.h> */
- int *wav; /* Number of waves for this individuual 0 is possible */
+ /* #endif */
- int maxwav; /* Maxim number of waves */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #include <time.h>
- int ijmin, ijmax; /* Individuals having jmin and jmax */
- int gipmx, gsw; /* Global variables on the number of contributions
+ #ifdef GSL
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #include <gsl/gsl_errno.h>
- int mle, weightopt;
+ #include <gsl/gsl_multimin.h>
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #endif
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #ifdef NLOPT
- double jmean; /* Mean space between 2 waves */
+ #include <nlopt.h>
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ typedef struct {
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+   double (* function)(double [] );
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ } myfunc_data ;
- FILE *ficlog, *ficrespow;
+ #endif
- int globpr; /* Global variable for printing or not */
- double fretone; /* Only one call to likelihood */
+ /* #include <libintl.h> */
- long ipmx; /* Number of contributions */
+ /* #define _(String) gettext (String) */
- double sw; /* Sum of weights */
- char filerespow[FILENAMELENGTH];
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- FILE *ficresilk;
+ #define GNUPLOTPROGRAM "gnuplot"
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- FILE *ficresprobmorprev;
+ #define FILENAMELENGTH 132
- FILE *fichtm, *fichtmcov; /* Html File */
- FILE *ficreseij;
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- char filerese[FILENAMELENGTH];
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- FILE *ficresstdeij;
- char fileresstde[FILENAMELENGTH];
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- FILE *ficrescveij;
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- char filerescve[FILENAMELENGTH];
- FILE  *ficresvij;
+ #define NINTERVMAX 8
- char fileresv[FILENAMELENGTH];
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- FILE  *ficresvpl;
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- char fileresvpl[FILENAMELENGTH];
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- char title[MAXLINE];
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ #define MAXN 20000
- char command[FILENAMELENGTH];
+ #define YEARM 12. /**< Number of months per year */
- int  outcmd=0;
+ /* #define AGESUP 130 */
+ #define AGESUP 150
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
+ #define AGEBASE 40
- char filelog[FILENAMELENGTH]; /* Log file */
+ #define AGEOVERFLOW 1.e20
- char filerest[FILENAMELENGTH];
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- char fileregp[FILENAMELENGTH];
+ #ifdef _WIN32
- char popfile[FILENAMELENGTH];
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ #define ODIRSEPARATOR '/'
+ #else
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ #define DIRSEPARATOR '/'
- struct timezone tzp;
+ #define CHARSEPARATOR "/"
- extern int gettimeofday();
+ #define ODIRSEPARATOR '\\'
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ #endif
- long time_value;
- extern long time();
+ /* $Id$ */
- char strcurr[80], strfor[80];
+ /* $State$ */
+ #include "version.h"
- char *endptr;
+ char version[]=__IMACH_VERSION__;
- long lval;
+ char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- double dval;
+ char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
- #define NR_END 1
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- #define FREE_ARG char*
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- #define FTOL 1.0e-10
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- #define NRANSI
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- #define ITMAX 200
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- #define TOL 2.0e-4
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- #define CGOLD 0.3819660
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- #define ZEPS 1.0e-10
+ int cptcov=0; /* Working variable */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
+ int npar=NPARMAX;
- #define GOLD 1.618034
+ int nlstate=2; /* Number of live states */
- #define GLIMIT 100.0
+ int ndeath=1; /* Number of dead states */
- #define TINY 1.0e-20
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int popbased=0;
- static double maxarg1,maxarg2;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ int *wav; /* Number of waves for this individuual 0 is possible */
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ int maxwav=0; /* Maxim number of waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- #define rint(a) floor(a+0.5)
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
- static double sqrarg;
+ int mle=1, weightopt=0;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- int agegomp= AGEGOMP;
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- int imx;
+ int countcallfunc=0;  /* Count the number of calls to func */
- int stepm=1;
+ double jmean=1; /* Mean space between 2 waves */
- /* Stepm, step in month: minimum step interpolation*/
+ double **matprod2(); /* test */
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- int estepm;
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
- int m,nb;
+ /*FILE *fic ; */ /* Used in readdata only */
- long *num;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ FILE *ficlog, *ficrespow;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ int globpr=0; /* Global variable for printing or not */
- double **pmmij, ***probs;
+ double fretone; /* Only one call to likelihood */
- double *ageexmed,*agecens;
+ long ipmx=0; /* Number of contributions */
- double dateintmean=0;
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
- double *weight;
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- int **s; /* Status */
+ FILE *ficresilk;
- double *agedc, **covar, idx;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ FILE *ficresprobmorprev;
- double *lsurv, *lpop, *tpop;
+ FILE *fichtm, *fichtmcov; /* Html File */
+ FILE *ficreseij;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ char filerese[FILENAMELENGTH];
- double ftolhess; /* Tolerance for computing hessian */
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
- /**************** split *************************/
+ FILE *ficrescveij;
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ char filerescve[FILENAMELENGTH];
- {
+ FILE  *ficresvij;
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ char fileresv[FILENAMELENGTH];
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ FILE  *ficresvpl;
-   */
+ char fileresvpl[FILENAMELENGTH];
-   char  *ss;                            /* pointer */
+ char title[MAXLINE];
-   int   l1, l2;                         /* length counters */
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
-   l1 = strlen(path );                   /* length of path */
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ char command[FILENAMELENGTH];
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ int  outcmd=0;
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ char filelog[FILENAMELENGTH]; /* Log file */
-     /* get current working directory */
+ char filerest[FILENAMELENGTH];
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ char fileregp[FILENAMELENGTH];
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ char popfile[FILENAMELENGTH];
-       return( GLOCK_ERROR_GETCWD );
-     }
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
-     /* got dirc from getcwd*/
-     printf(" DIRC = %s \n",dirc);
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
-   } else {                              /* strip direcotry from path */
+ /* struct timezone tzp; */
-     ss++;                               /* after this, the filename */
+ /* extern int gettimeofday(); */
-     l2 = strlen( ss );                  /* length of filename */
+ struct tm tml, *gmtime(), *localtime();
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-     strcpy( name, ss );         /* save file name */
+ extern time_t time();
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     dirc[l1-l2] = 0;                    /* add zero */
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
-     printf(" DIRC2 = %s \n",dirc);
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
-   }
+ struct tm tm;
-   /* We add a separator at the end of dirc if not exists */
-   l1 = strlen( dirc );                  /* length of directory */
+ char strcurr[80], strfor[80];
-   if( dirc[l1-1] != DIRSEPARATOR ){
-     dirc[l1] =  DIRSEPARATOR;
+ char *endptr;
-     dirc[l1+1] = 0;
+ long lval;
-     printf(" DIRC3 = %s \n",dirc);
+ double dval;
-   }
-   ss = strrchr( name, '.' );            /* find last / */
+ #define NR_END 1
-   if (ss >0){
+ #define FREE_ARG char*
-     ss++;
+ #define FTOL 1.0e-10
-     strcpy(ext,ss);                     /* save extension */
-     l1= strlen( name);
+ #define NRANSI
-     l2= strlen(ss)+1;
+ #define ITMAX 200
-     strncpy( finame, name, l1-l2);
-     finame[l1-l2]= 0;
+ #define TOL 2.0e-4
-   }
+ #define CGOLD 0.3819660
-   return( 0 );                          /* we're done */
+ #define ZEPS 1.0e-10
- }
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ #define GOLD 1.618034
- /******************************************/
+ #define GLIMIT 100.0
+ #define TINY 1.0e-20
- void replace_back_to_slash(char *s, char*t)
- {
+ static double maxarg1,maxarg2;
-   int i;
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-   int lg=0;
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-   i=0;
-   lg=strlen(t);
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   for(i=0; i<= lg; i++) {
+ #define rint(a) floor(a+0.5)
-     (s[i] = t[i]);
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     if (t[i]== '\\') s[i]='/';
+ #define mytinydouble 1.0e-16
-   }
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
- }
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
+ /* static double dsqrarg; */
- int nbocc(char *s, char occ)
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
- {
+ static double sqrarg;
-   int i,j=0;
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   int lg=20;
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   i=0;
+ int agegomp= AGEGOMP;
-   lg=strlen(s);
-   for(i=0; i<= lg; i++) {
+ int imx;
-   if  (s[i] == occ ) j++;
+ int stepm=1;
-   }
+ /* Stepm, step in month: minimum step interpolation*/
-   return j;
- }
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- void cutv(char *u,char *v, char*t, char occ)
- {
+ int m,nb;
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ long *num;
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ int firstpass=0, lastpass=4,*cod, *cens;
-      gives u="abcedf" and v="ghi2j" */
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
-   int i,lg,j,p=0;
+                    covariate for which somebody answered excluding
-   i=0;
+                    undefined. Usually 2: 0 and 1. */
-   for(j=0; j<=strlen(t)-1; j++) {
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+                              covariate for which somebody answered including
-   }
+                              undefined. Usually 3: -1, 0 and 1. */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-   lg=strlen(t);
+ double **pmmij, ***probs; /* Global pointer */
-   for(j=0; j<p; j++) {
+ double ***mobaverage, ***mobaverages; /* New global variable */
-     (u[j] = t[j]);
+ double *ageexmed,*agecens;
-   }
+ double dateintmean=0;
-      u[p]='\0';
+ double *weight;
-    for(j=0; j<= lg; j++) {
+ int **s; /* Status */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ double *agedc;
-   }
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
- }
+                   * covar=matrix(0,NCOVMAX,1,n);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
- /********************** nrerror ********************/
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- void nrerror(char error_text[])
+ int *Tage;
- {
+ int *Ndum; /** Freq of modality (tricode */
-   fprintf(stderr,"ERREUR ...\n");
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
-   fprintf(stderr,"%s\n",error_text);
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
-   exit(EXIT_FAILURE);
+ double *lsurv, *lpop, *tpop;
- }
- /*********************** vector *******************/
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- double *vector(int nl, int nh)
+ double ftolhess; /**< Tolerance for computing hessian */
- {
-   double *v;
+ /**************** split *************************/
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   if (!v) nrerror("allocation failure in vector");
+ {
-   return v-nl+NR_END;
+   /* 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)
+   */
- /************************ free vector ******************/
+   char  *ss;                            /* pointer */
- void free_vector(double*v, int nl, int nh)
+   int   l1=0, l2=0;                             /* length counters */
- {
-   free((FREE_ARG)(v+nl-NR_END));
+   l1 = strlen(path );                   /* length of path */
- }
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- /************************ivector *******************************/
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
- int *ivector(long nl,long nh)
+     strcpy( name, path );               /* we got the fullname name because no directory */
- {
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   int *v;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+     /* get current working directory */
-   if (!v) nrerror("allocation failure in ivector");
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   return v-nl+NR_END;
+ #ifdef WIN32
- }
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #else
- /******************free ivector **************************/
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
- void free_ivector(int *v, long nl, long nh)
+ #endif
- {
+       return( GLOCK_ERROR_GETCWD );
-   free((FREE_ARG)(v+nl-NR_END));
+     }
- }
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
- /************************lvector *******************************/
+   } else {                              /* strip directory from path */
- long *lvector(long nl,long nh)
+     ss++;                               /* after this, the filename */
- {
+     l2 = strlen( ss );                  /* length of filename */
-   long *v;
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+     strcpy( name, ss );         /* save file name */
-   if (!v) nrerror("allocation failure in ivector");
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   return v-nl+NR_END;
+     dirc[l1-l2] = '\0';                 /* add zero */
- }
+     printf(" DIRC2 = %s \n",dirc);
+   }
- /******************free lvector **************************/
+   /* We add a separator at the end of dirc if not exists */
- void free_lvector(long *v, long nl, long nh)
+   l1 = strlen( dirc );                  /* length of directory */
- {
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   free((FREE_ARG)(v+nl-NR_END));
+     dirc[l1] =  DIRSEPARATOR;
- }
+     dirc[l1+1] = 0;
+     printf(" DIRC3 = %s \n",dirc);
- /******************* imatrix *******************************/
+   }
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   ss = strrchr( name, '.' );            /* find last / */
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   if (ss >0){
- {
+     ss++;
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+     strcpy(ext,ss);                     /* save extension */
-   int **m;
+     l1= strlen( name);
+     l2= strlen(ss)+1;
-   /* allocate pointers to rows */
+     strncpy( finame, name, l1-l2);
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+     finame[l1-l2]= 0;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   }
-   m += NR_END;
-   m -= nrl;
+   return( 0 );                          /* we're done */
+ }
-   /* allocate rows and set pointers to them */
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ /******************************************/
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+ void replace_back_to_slash(char *s, char*t)
-   m[nrl] -= ncl;
+ {
+   int i;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   int lg=0;
+   i=0;
-   /* return pointer to array of pointers to rows */
+   lg=strlen(t);
-   return m;
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- /****************** free_imatrix *************************/
+   }
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ }
-       int **m;
-       long nch,ncl,nrh,nrl;
+ char *trimbb(char *out, char *in)
-      /* free an int matrix allocated by imatrix() */
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
- {
+   char *s;
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   s=out;
-   free((FREE_ARG) (m+nrl-NR_END));
+   while (*in != '\0'){
- }
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
- /******************* matrix *******************************/
+     }
- double **matrix(long nrl, long nrh, long ncl, long nch)
+     *out++ = *in++;
- {
+   }
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   *out='\0';
-   double **m;
+   return s;
+ }
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /* char *substrchaine(char *out, char *in, char *chain) */
-   m += NR_END;
+ /* { */
-   m -= nrl;
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+ /*   char *s, *t; */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   t=in;s=out; */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   while ((*in != *chain) && (*in != '\0')){ */
-   m[nrl] += NR_END;
+ /*     *out++ = *in++; */
-   m[nrl] -= ncl;
+ /*   } */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*   /\* *in matches *chain *\/ */
-   return m;
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-    */
+ /*   } */
- }
+ /*   in--; chain--; */
+ /*   while ( (*in != '\0')){ */
- /*************************free matrix ************************/
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ /*     *out++ = *in++; */
- {
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ /*   } */
-   free((FREE_ARG)(m+nrl-NR_END));
+ /*   *out='\0'; */
- }
+ /*   out=s; */
+ /*   return out; */
- /******************* ma3x *******************************/
+ /* } */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ char *substrchaine(char *out, char *in, char *chain)
  {
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   /* Substract chain 'chain' from 'in', return and output 'out' */
-   double ***m;
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   char *strloc;
-   if (!m) nrerror("allocation failure 1 in matrix()");
-   m += NR_END;
+   strcpy (out, in);
-   m -= nrl;
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   if(strloc != NULL){
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
-   m[nrl] += NR_END;
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
-   m[nrl] -= ncl;
+     /* strcpy (strloc, strloc +strlen(chain));*/
+   }
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   return out;
-   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;
-   m[nrl][ncl] -= nll;
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-   for (j=ncl+1; j<=nch; j++)
+ {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   for (i=nrl+1; i<=nrh; i++) {
+      gives blocc="abcdef" and alocc="ghi2j".
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-     for (j=ncl+1; j<=nch; j++)
+   */
-       m[i][j]=m[i][j-1]+nlay;
+   char *s, *t;
-   }
+   t=in;s=in;
-   return m;
+   while ((*in != occ) && (*in != '\0')){
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+     *alocc++ = *in++;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   }
-   */
+   if( *in == occ){
- }
+     *(alocc)='\0';
+     s=++in;
- /*************************free ma3x ************************/
+   }
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
- {
+   if (s == t) {/* occ not found */
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+     *(alocc-(in-s))='\0';
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+     in=s;
-   free((FREE_ARG)(m+nrl-NR_END));
+   }
- }
+   while ( *in != '\0'){
+     *blocc++ = *in++;
- /*************** function subdirf ***********/
+   }
- char *subdirf(char fileres[])
- {
+   *blocc='\0';
-   /* Caution optionfilefiname is hidden */
+   return t;
-   strcpy(tmpout,optionfilefiname);
+ }
-   strcat(tmpout,"/"); /* Add to the right */
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   strcat(tmpout,fileres);
+ {
-   return tmpout;
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
- }
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
- /*************** function subdirf2 ***********/
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
- char *subdirf2(char fileres[], char *preop)
+   */
- {
+   char *s, *t;
+   t=in;s=in;
-   /* Caution optionfilefiname is hidden */
+   while (*in != '\0'){
-   strcpy(tmpout,optionfilefiname);
+     while( *in == occ){
-   strcat(tmpout,"/");
+       *blocc++ = *in++;
-   strcat(tmpout,preop);
+       s=in;
-   strcat(tmpout,fileres);
+     }
-   return tmpout;
+     *blocc++ = *in++;
- }
+   }
+   if (s == t) /* occ not found */
- /*************** function subdirf3 ***********/
+     *(blocc-(in-s))='\0';
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   else
- {
+     *(blocc-(in-s)-1)='\0';
+   in=s;
-   /* Caution optionfilefiname is hidden */
+   while ( *in != '\0'){
-   strcpy(tmpout,optionfilefiname);
+     *alocc++ = *in++;
-   strcat(tmpout,"/");
+   }
-   strcat(tmpout,preop);
-   strcat(tmpout,preop2);
+   *alocc='\0';
-   strcat(tmpout,fileres);
+   return s;
-   return tmpout;
+ }
- }
+ int nbocc(char *s, char occ)
- /***************** f1dim *************************/
+ {
- extern int ncom;
+   int i,j=0;
- extern double *pcom,*xicom;
+   int lg=20;
- extern double (*nrfunc)(double []);
+   i=0;
+   lg=strlen(s);
- double f1dim(double x)
+   for(i=0; i<= lg; i++) {
- {
+   if  (s[i] == occ ) j++;
-   int j;
+   }
-   double f;
+   return j;
-   double *xt;
+ }
-   xt=vector(1,ncom);
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ /* { */
-   f=(*nrfunc)(xt);
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   free_vector(xt,1,ncom);
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   return f;
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
- }
+ /*   int i,lg,j,p=0; */
+ /*   i=0; */
- /*****************brent *************************/
+ /*   lg=strlen(t); */
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+ /*   for(j=0; j<=lg-1; j++) { */
- {
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   int iter;
+ /*   } */
-   double a,b,d,etemp;
-   double fu,fv,fw,fx;
+ /*   for(j=0; j<p; j++) { */
-   double ftemp;
+ /*     (u[j] = t[j]); */
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ /*   } */
-   double e=0.0;
+ /*      u[p]='\0'; */
-   a=(ax < cx ? ax : cx);
+ /*    for(j=0; j<= lg; j++) { */
-   b=(ax > cx ? ax : cx);
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   x=w=v=bx;
+ /*   } */
-   fw=fv=fx=(*f)(x);
+ /* } */
-   for (iter=1;iter<=ITMAX;iter++) {
-     xm=0.5*(a+b);
+ #ifdef _WIN32
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ char * strsep(char **pp, const char *delim)
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ {
-     printf(".");fflush(stdout);
+   char *p, *q;
-     fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+   if ((p = *pp) == NULL)
-     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);
+     return 0;
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   if ((q = strpbrk (p, delim)) != NULL)
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   {
- #endif
+     *pp = q + 1;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+     *q = '\0';
-       *xmin=x;
+   }
-       return fx;
+   else
-     }
+     *pp = 0;
-     ftemp=fu;
+   return p;
-     if (fabs(e) > tol1) {
+ }
-       r=(x-w)*(fx-fv);
+ #endif
-       q=(x-v)*(fx-fw);
-       p=(x-v)*q-(x-w)*r;
+ /********************** nrerror ********************/
-       q=2.0*(q-r);
-       if (q > 0.0) p = -p;
+ void nrerror(char error_text[])
-       q=fabs(q);
+ {
-       etemp=e;
+   fprintf(stderr,"ERREUR ...\n");
-       e=d;
+   fprintf(stderr,"%s\n",error_text);
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   exit(EXIT_FAILURE);
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ }
-       else {
+ /*********************** vector *******************/
-         d=p/q;
+ double *vector(int nl, int nh)
-         u=x+d;
+ {
-         if (u-a < tol2 || b-u < tol2)
+   double *v;
-           d=SIGN(tol1,xm-x);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-       }
+   if (!v) nrerror("allocation failure in vector");
-     } else {
+   return v-nl+NR_END;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ }
-     }
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ /************************ free vector ******************/
-     fu=(*f)(u);
+ void free_vector(double*v, int nl, int nh)
-     if (fu <= fx) {
+ {
-       if (u >= x) a=x; else b=x;
+   free((FREE_ARG)(v+nl-NR_END));
-       SHFT(v,w,x,u)
+ }
-         SHFT(fv,fw,fx,fu)
-         } else {
+ /************************ivector *******************************/
-           if (u < x) a=u; else b=u;
+ int *ivector(long nl,long nh)
-           if (fu <= fw || w == x) {
+ {
-             v=w;
+   int *v;
-             w=u;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-             fv=fw;
+   if (!v) nrerror("allocation failure in ivector");
-             fw=fu;
+   return v-nl+NR_END;
-           } else if (fu <= fv || v == x || v == w) {
+ }
-             v=u;
-             fv=fu;
+ /******************free ivector **************************/
-           }
+ void free_ivector(int *v, long nl, long nh)
-         }
+ {
-   }
+   free((FREE_ARG)(v+nl-NR_END));
-   nrerror("Too many iterations in brent");
+ }
-   *xmin=x;
-   return fx;
+ /************************lvector *******************************/
- }
+ long *lvector(long nl,long nh)
+ {
- /****************** mnbrak ***********************/
+   long *v;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   if (!v) nrerror("allocation failure in ivector");
-             double (*func)(double))
+   return v-nl+NR_END;
- {
+ }
-   double ulim,u,r,q, dum;
-   double fu;
+ /******************free lvector **************************/
+ void free_lvector(long *v, long nl, long nh)
-   *fa=(*func)(*ax);
+ {
-   *fb=(*func)(*bx);
+   free((FREE_ARG)(v+nl-NR_END));
-   if (*fb > *fa) {
+ }
-     SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+ /******************* imatrix *******************************/
-       }
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   *cx=(*bx)+GOLD*(*bx-*ax);
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   *fc=(*func)(*cx);
+ {
-   while (*fb > *fc) {
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-     r=(*bx-*ax)*(*fb-*fc);
+   int **m;
-     q=(*bx-*cx)*(*fb-*fa);
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   /* allocate pointers to rows */
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   m += NR_END;
-       fu=(*func)(u);
+   m -= nrl;
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       fu=(*func)(u);
-       if (fu < *fc) {
+   /* allocate rows and set pointers to them */
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-           SHFT(*fb,*fc,fu,(*func)(u))
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-           }
+   m[nrl] += NR_END;
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   m[nrl] -= ncl;
-       u=ulim;
-       fu=(*func)(u);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     } else {
-       u=(*cx)+GOLD*(*cx-*bx);
+   /* return pointer to array of pointers to rows */
-       fu=(*func)(u);
+   return m;
-     }
+ }
-     SHFT(*ax,*bx,*cx,u)
-       SHFT(*fa,*fb,*fc,fu)
+ /****************** free_imatrix *************************/
-       }
+ void free_imatrix(m,nrl,nrh,ncl,nch)
- }
+       int **m;
+       long nch,ncl,nrh,nrl;
- /*************** linmin ************************/
+      /* free an int matrix allocated by imatrix() */
+ {
- int ncom;
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
- double *pcom,*xicom;
+   free((FREE_ARG) (m+nrl-NR_END));
- double (*nrfunc)(double []);
+ }
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ /******************* matrix *******************************/
- {
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-   double brent(double ax, double bx, double cx,
+ {
-                double (*f)(double), double tol, double *xmin);
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-   double f1dim(double x);
+   double **m;
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-               double *fc, double (*func)(double));
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   int j;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   double xx,xmin,bx,ax;
+   m += NR_END;
-   double fx,fb,fa;
+   m -= nrl;
-   ncom=n;
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   pcom=vector(1,n);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   xicom=vector(1,n);
+   m[nrl] += NR_END;
-   nrfunc=func;
+   m[nrl] -= ncl;
-   for (j=1;j<=n;j++) {
-     pcom[j]=p[j];
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     xicom[j]=xi[j];
+   return m;
-   }
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-   ax=0.0;
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-   xx=1.0;
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+    */
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ }
- #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ /*************************free matrix ************************/
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
- #endif
+ {
-   for (j=1;j<=n;j++) {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     xi[j] *= xmin;
+   free((FREE_ARG)(m+nrl-NR_END));
-     p[j] += xi[j];
+ }
-   }
-   free_vector(xicom,1,n);
+ /******************* ma3x *******************************/
-   free_vector(pcom,1,n);
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
- }
+ {
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
- char *asc_diff_time(long time_sec, char ascdiff[])
+   double ***m;
- {
-   long sec_left, days, hours, minutes;
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   days = (time_sec) / (60*60*24);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   sec_left = (time_sec) % (60*60*24);
+   m += NR_END;
-   hours = (sec_left) / (60*60) ;
+   m -= nrl;
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   sec_left = (sec_left) % (60);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   m[nrl] += NR_END;
-   return ascdiff;
+   m[nrl] -= ncl;
- }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- /*************** powell ************************/
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-             double (*func)(double []))
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
- {
+   m[nrl][ncl] += NR_END;
-   void linmin(double p[], double xi[], int n, double *fret,
+   m[nrl][ncl] -= nll;
-               double (*func)(double []));
+   for (j=ncl+1; j<=nch; j++)
-   int i,ibig,j;
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   double del,t,*pt,*ptt,*xit;
-   double fp,fptt;
+   for (i=nrl+1; i<=nrh; i++) {
-   double *xits;
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   int niterf, itmp;
+     for (j=ncl+1; j<=nch; j++)
+       m[i][j]=m[i][j-1]+nlay;
-   pt=vector(1,n);
+   }
-   ptt=vector(1,n);
+   return m;
-   xit=vector(1,n);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   xits=vector(1,n);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   *fret=(*func)(p);
+   */
-   for (j=1;j<=n;j++) pt[j]=p[j];
+ }
-   for (*iter=1;;++(*iter)) {
-     fp=(*fret);
+ /*************************free ma3x ************************/
-     ibig=0;
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-     del=0.0;
+ {
-     last_time=curr_time;
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-     (void) gettimeofday(&curr_time,&tzp);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     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);
+   free((FREE_ARG)(m+nrl-NR_END));
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+ }
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-    for (i=1;i<=n;i++) {
+ /*************** function subdirf ***********/
-       printf(" %d %.12f",i, p[i]);
+ char *subdirf(char fileres[])
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+ {
-       fprintf(ficrespow," %.12lf", p[i]);
+   /* Caution optionfilefiname is hidden */
-     }
+   strcpy(tmpout,optionfilefiname);
-     printf("\n");
+   strcat(tmpout,"/"); /* Add to the right */
-     fprintf(ficlog,"\n");
+   strcat(tmpout,fileres);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   return tmpout;
-     if(*iter <=3){
+ }
-       tm = *localtime(&curr_time.tv_sec);
-       strcpy(strcurr,asctime(&tm));
+ /*************** function subdirf2 ***********/
- /*       asctime_r(&tm,strcurr); */
+ char *subdirf2(char fileres[], char *preop)
-       forecast_time=curr_time;
+ {
-       itmp = strlen(strcurr);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   /* Caution optionfilefiname is hidden */
-         strcurr[itmp-1]='\0';
+   strcpy(tmpout,optionfilefiname);
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   strcat(tmpout,"/");
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   strcat(tmpout,preop);
-       for(niterf=10;niterf<=30;niterf+=10){
+   strcat(tmpout,fileres);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+   return tmpout;
-         tmf = *localtime(&forecast_time.tv_sec);
+ }
- /*      asctime_r(&tmf,strfor); */
-         strcpy(strfor,asctime(&tmf));
+ /*************** function subdirf3 ***********/
-         itmp = strlen(strfor);
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-         if(strfor[itmp-1]=='\n')
+ {
-         strfor[itmp-1]='\0';
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   /* Caution optionfilefiname is hidden */
-         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);
+   strcpy(tmpout,optionfilefiname);
-       }
+   strcat(tmpout,"/");
-     }
+   strcat(tmpout,preop);
-     for (i=1;i<=n;i++) {
+   strcat(tmpout,preop2);
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   strcat(tmpout,fileres);
-       fptt=(*fret);
+   return tmpout;
- #ifdef DEBUG
+ }
-       printf("fret=%lf \n",*fret);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+ /*************** function subdirfext ***********/
- #endif
+ char *subdirfext(char fileres[], char *preop, char *postop)
-       printf("%d",i);fflush(stdout);
+ {
-       fprintf(ficlog,"%d",i);fflush(ficlog);
-       linmin(p,xit,n,fret,func);
+   strcpy(tmpout,preop);
-       if (fabs(fptt-(*fret)) > del) {
+   strcat(tmpout,fileres);
-         del=fabs(fptt-(*fret));
+   strcat(tmpout,postop);
-         ibig=i;
+   return tmpout;
-       }
+ }
- #ifdef DEBUG
-       printf("%d %.12e",i,(*fret));
+ /*************** function subdirfext3 ***********/
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+ char *subdirfext3(char fileres[], char *preop, char *postop)
-       for (j=1;j<=n;j++) {
+ {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf(" x(%d)=%.12e",j,xit[j]);
+   /* Caution optionfilefiname is hidden */
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   strcpy(tmpout,optionfilefiname);
-       }
+   strcat(tmpout,"/");
-       for(j=1;j<=n;j++) {
+   strcat(tmpout,preop);
-         printf(" p=%.12e",p[j]);
+   strcat(tmpout,fileres);
-         fprintf(ficlog," p=%.12e",p[j]);
+   strcat(tmpout,postop);
-       }
+   return tmpout;
-       printf("\n");
+ }
-       fprintf(ficlog,"\n");
- #endif
+ char *asc_diff_time(long time_sec, char ascdiff[])
-     }
+ {
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   long sec_left, days, hours, minutes;
- #ifdef DEBUG
+   days = (time_sec) / (60*60*24);
-       int k[2],l;
+   sec_left = (time_sec) % (60*60*24);
-       k[0]=1;
+   hours = (sec_left) / (60*60) ;
-       k[1]=-1;
+   sec_left = (sec_left) %(60*60);
-       printf("Max: %.12e",(*func)(p));
+   minutes = (sec_left) /60;
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   sec_left = (sec_left) % (60);
-       for (j=1;j<=n;j++) {
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-         printf(" %.12e",p[j]);
+   return ascdiff;
-         fprintf(ficlog," %.12e",p[j]);
+ }
-       }
-       printf("\n");
+ /***************** f1dim *************************/
-       fprintf(ficlog,"\n");
+ extern int ncom;
-       for(l=0;l<=1;l++) {
+ extern double *pcom,*xicom;
-         for (j=1;j<=n;j++) {
+ extern double (*nrfunc)(double []);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ double f1dim(double x)
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ {
-         }
+   int j;
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   double f;
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   double *xt;
-       }
- #endif
+   xt=vector(1,ncom);
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   f=(*nrfunc)(xt);
-       free_vector(xit,1,n);
+   free_vector(xt,1,ncom);
-       free_vector(xits,1,n);
+   return f;
-       free_vector(ptt,1,n);
+ }
-       free_vector(pt,1,n);
-       return;
+ /*****************brent *************************/
-     }
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ {
-     for (j=1;j<=n;j++) {
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       ptt[j]=2.0*p[j]-pt[j];
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-       xit[j]=p[j]-pt[j];
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
-       pt[j]=p[j];
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
-     }
+    * returned function value.
-     fptt=(*func)(ptt);
+   */
-     if (fptt < fp) {
+   int iter;
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+   double a,b,d,etemp;
-       if (t < 0.0) {
+   double fu=0,fv,fw,fx;
-         linmin(p,xit,n,fret,func);
+   double ftemp=0.;
-         for (j=1;j<=n;j++) {
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-           xi[j][ibig]=xi[j][n];
+   double e=0.0;
-           xi[j][n]=xit[j];
-         }
+   a=(ax < cx ? ax : cx);
- #ifdef DEBUG
+   b=(ax > cx ? ax : cx);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   x=w=v=bx;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   fw=fv=fx=(*f)(x);
-         for(j=1;j<=n;j++){
+   for (iter=1;iter<=ITMAX;iter++) {
-           printf(" %.12e",xit[j]);
+     xm=0.5*(a+b);
-           fprintf(ficlog," %.12e",xit[j]);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-         }
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-         printf("\n");
+     printf(".");fflush(stdout);
-         fprintf(ficlog,"\n");
+     fprintf(ficlog,".");fflush(ficlog);
- #endif
+ #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);
-     }
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-   }
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- }
+ #endif
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
- /**** Prevalence limit (stable or period prevalence)  ****************/
+       *xmin=x;
+       return fx;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+     }
- {
+     ftemp=fu;
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+     if (fabs(e) > tol1) {
-      matrix by transitions matrix until convergence is reached */
+       r=(x-w)*(fx-fv);
+       q=(x-v)*(fx-fw);
-   int i, ii,j,k;
+       p=(x-v)*q-(x-w)*r;
-   double min, max, maxmin, maxmax,sumnew=0.;
+       q=2.0*(q-r);
-   double **matprod2();
+       if (q > 0.0) p = -p;
-   double **out, cov[NCOVMAX], **pmij();
+       q=fabs(q);
-   double **newm;
+       etemp=e;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+       e=d;
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     for (j=1;j<=nlstate+ndeath;j++){
+       else {
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         d=p/q;
-     }
+         u=x+d;
+         if (u-a < tol2 || b-u < tol2)
-    cov[1]=1.;
+           d=SIGN(tol1,xm-x);
+       }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+     } else {
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     newm=savm;
+     }
-     /* Covariates have to be included here again */
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-      cov[2]=agefin;
+     fu=(*f)(u);
+     if (fu <= fx) {
-       for (k=1; k<=cptcovn;k++) {
+       if (u >= x) a=x; else b=x;
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       SHFT(v,w,x,u)
-         /*      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]]);*/
+       SHFT(fv,fw,fx,fu)
-       }
+     } else {
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       if (u < x) a=u; else b=u;
-       for (k=1; k<=cptcovprod;k++)
+       if (fu <= fw || w == x) {
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         v=w;
+         w=u;
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+         fv=fw;
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+         fw=fu;
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+       } else if (fu <= fv || v == x || v == w) {
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+         v=u;
+         fv=fu;
-     savm=oldm;
+       }
-     oldm=newm;
+     }
-     maxmax=0.;
+   }
-     for(j=1;j<=nlstate;j++){
+   nrerror("Too many iterations in brent");
-       min=1.;
+   *xmin=x;
-       max=0.;
+   return fx;
-       for(i=1; i<=nlstate; i++) {
+ }
-         sumnew=0;
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+ /****************** mnbrak ***********************/
-         prlim[i][j]= newm[i][j]/(1-sumnew);
-         max=FMAX(max,prlim[i][j]);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         min=FMIN(min,prlim[i][j]);
+             double (*func)(double))
-       }
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
-       maxmin=max-min;
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
-       maxmax=FMAX(maxmax,maxmin);
+ 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.
-     if(maxmax < ftolpl){
+    */
-       return prlim;
+   double ulim,u,r,q, dum;
-     }
+   double fu;
-   }
- }
+   double scale=10.;
+   int iterscale=0;
- /*************** transition probabilities ***************/
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
- {
-   double s1, s2;
-   /*double t34;*/
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
-   int i,j,j1, nc, ii, jj;
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-     for(i=1; i<= nlstate; i++){
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
-       for(j=1; j<i;j++){
+   /* } */
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-           /*s2 += param[i][j][nc]*cov[nc];*/
+   if (*fb > *fa) {
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+     SHFT(dum,*ax,*bx,dum)
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+     SHFT(dum,*fb,*fa,dum)
-         }
+   }
-         ps[i][j]=s2;
+   *cx=(*bx)+GOLD*(*bx-*ax);
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+   *fc=(*func)(*cx);
-       }
+ #ifdef DEBUG
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ #endif
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
-         }
+     r=(*bx-*ax)*(*fb-*fc);
-         ps[i][j]=s2;
+     q=(*bx-*cx)*(*fb-*fa);
-       }
+     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). */
-     /*ps[3][2]=1;*/
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-     for(i=1; i<= nlstate; i++){
+       fu=(*func)(u);
-       s1=0;
+ #ifdef DEBUG
-       for(j=1; j<i; j++)
+       /* f(x)=A(x-u)**2+f(u) */
-         s1+=exp(ps[i][j]);
+       double A, fparabu;
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         s1+=exp(ps[i][j]);
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-       ps[i][i]=1./(s1+1.);
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-       for(j=1; j<i; j++)
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-     } /* end i */
+ #endif
+ #ifdef MNBRAKORIGINAL
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ #else
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+ /*       if (fu > *fc) { */
-         ps[ii][jj]=0;
+ /* #ifdef DEBUG */
-         ps[ii][ii]=1;
+ /*       printf("mnbrak4  fu > fc \n"); */
-       }
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
-     }
+ /* #endif */
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+ /*      dum=u; /\* Shifting c and u *\/ */
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ /*      u = *cx; */
- /*         printf("ddd %lf ",ps[ii][jj]); */
+ /*      *cx = dum; */
- /*       } */
+ /*      dum = fu; */
- /*       printf("\n "); */
+ /*      fu = *fc; */
- /*        } */
+ /*      *fc =dum; */
- /*        printf("\n ");printf("%lf ",cov[2]); */
+ /*       } else { /\* end *\/ */
-        /*
+ /* #ifdef DEBUG */
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ /*       printf("mnbrak3  fu < fc \n"); */
-       goto end;*/
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-     return ps;
+ /* #endif */
- }
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
- /**************** Product of 2 matrices ******************/
+ /*      *cx = dum; */
+ /*      dum = fu; */
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ /*      fu = *fc; */
- {
+ /*      *fc =dum; */
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ /*       } */
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+ #ifdef DEBUG
-   /* in, b, out are matrice of pointers which should have been initialized
+       printf("mnbrak34  fu < or >= fc \n");
-      before: only the contents of out is modified. The function returns
+       fprintf(ficlog, "mnbrak34 fu < fc\n");
-      a pointer to pointers identical to out */
+ #endif
-   long i, j, k;
+       dum=u; /* Shifting c and u */
-   for(i=nrl; i<= nrh; i++)
+       u = *cx;
-     for(k=ncolol; k<=ncoloh; k++)
+       *cx = dum;
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       dum = fu;
-         out[i][k] +=in[i][j]*b[j][k];
+       fu = *fc;
+       *fc =dum;
-   return out;
+ #endif
- }
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+ #ifdef DEBUG
+       printf("mnbrak2  u after c but before ulim\n");
- /************* Higher Matrix Product ***************/
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
+ #endif
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       fu=(*func)(u);
- {
+       if (fu < *fc) {
-   /* Computes the transition matrix starting at age 'age' over
+ #ifdef DEBUG
-      'nhstepm*hstepm*stepm' months (i.e. until
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
-      nhstepm*hstepm matrices.
+ #endif
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-      (typically every 2 years instead of every month which is too big
+         SHFT(*fb,*fc,fu,(*func)(u))
-      for the memory).
+       }
-      Model is determined by parameters x and covariates have to be
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-      included manually here.
+ #ifdef DEBUG
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
-      */
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
+ #endif
-   int i, j, d, h, k;
+       u=ulim;
-   double **out, cov[NCOVMAX];
+       fu=(*func)(u);
-   double **newm;
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
+ #ifdef DEBUG
-   /* Hstepm could be zero and should return the unit matrix */
+       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
-   for (i=1;i<=nlstate+ndeath;i++)
+       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
-     for (j=1;j<=nlstate+ndeath;j++){
+ #endif
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       u=(*cx)+GOLD*(*cx-*bx);
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       fu=(*func)(u);
-     }
+     } /* end tests */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+     SHFT(*ax,*bx,*cx,u)
-   for(h=1; h <=nhstepm; h++){
+     SHFT(*fa,*fb,*fc,fu)
-     for(d=1; d <=hstepm; d++){
+ #ifdef DEBUG
-       newm=savm;
+       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
-       /* Covariates have to be included here again */
+       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
-       cov[1]=1.;
+ #endif
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ }
-       for (k=1; k<=cptcovage;k++)
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ /*************** linmin ************************/
-       for (k=1; k<=cptcovprod;k++)
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
+ the value of func at the returned location p . This is actually all accomplished by calling the
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+ routines mnbrak and brent .*/
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+ int ncom;
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+ double *pcom,*xicom;
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ double (*nrfunc)(double []);
-       savm=oldm;
-       oldm=newm;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-     }
+ {
-     for(i=1; i<=nlstate+ndeath; i++)
+   double brent(double ax, double bx, double cx,
-       for(j=1;j<=nlstate+ndeath;j++) {
+                double (*f)(double), double tol, double *xmin);
-         po[i][j][h]=newm[i][j];
+   double f1dim(double x);
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-          */
+               double *fc, double (*func)(double));
-       }
+   int j;
-   } /* end h */
+   double xx,xmin,bx,ax;
-   return po;
+   double fx,fb,fa;
- }
+ #ifdef LINMINORIGINAL
+ #else
- /*************** log-likelihood *************/
+   double scale=10., axs, xxs; /* Scale added for infinity */
- double func( double *x)
+ #endif
- {
-   int i, ii, j, k, mi, d, kk;
+   ncom=n;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   pcom=vector(1,n);
-   double **out;
+   xicom=vector(1,n);
-   double sw; /* Sum of weights */
+   nrfunc=func;
-   double lli; /* Individual log likelihood */
+   for (j=1;j<=n;j++) {
-   int s1, s2;
+     pcom[j]=p[j];
-   double bbh, survp;
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
-   long ipmx;
+   }
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+ #ifdef LINMINORIGINAL
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   xx=1.;
-   /*for(i=1;i<imx;i++)
+ #else
-     printf(" %d\n",s[4][i]);
+   axs=0.0;
-   */
+   xxs=1.;
-   cov[1]=1.;
+   do{
+     xx= xxs;
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ #endif
+     ax=0.;
-   if(mle==1){
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     /* 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))   */
-       for(mi=1; mi<= wav[i]-1; mi++){
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
-           for (j=1;j<=nlstate+ndeath;j++){
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* 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]]*/
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef LINMINORIGINAL
-           }
+ #else
-         for(d=0; d<dh[mi][i]; d++){
+     if (fx != fx){
-           newm=savm;
+         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         printf("|");
-           for (kk=1; kk<=cptcovage;kk++) {
+         fprintf(ficlog,"|");
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef DEBUGLINMIN
-           }
+         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ #endif
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
+   }while(fx != fx);
-           oldm=newm;
+ #endif
-         } /* end mult */
+ #ifdef DEBUGLINMIN
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+   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);
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+   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);
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+ #endif
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+   /* fmin = f(p[j] + xmin * xi[j]) */
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
-          * probability in order to take into account the bias as a fraction of the way
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+ #ifdef DEBUG
-          * -stepm/2 to stepm/2 .
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-          * For stepm=1 the results are the same as for previous versions of Imach.
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-          * For stepm > 1 the results are less biased than in previous versions.
+ #endif
-          */
+ #ifdef DEBUGLINMIN
-         s1=s[mw[mi][i]][i];
+   printf("linmin end ");
-         s2=s[mw[mi+1][i]][i];
+   fprintf(ficlog,"linmin end ");
-         bbh=(double)bh[mi][i]/(double)stepm;
+ #endif
-         /* bias bh is positive if real duration
+   for (j=1;j<=n;j++) {
-          * is higher than the multiple of stepm and negative otherwise.
+ #ifdef LINMINORIGINAL
-          */
+     xi[j] *= xmin;
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+ #else
-         if( s2 > nlstate){
+ #ifdef DEBUGLINMIN
-           /* i.e. if s2 is a death state and if the date of death is known
+     if(xxs <1.0)
-              then the contribution to the likelihood is the probability to
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
-              die between last step unit time and current  step unit time,
+ #endif
-              which is also equal to probability to die before dh
+     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) */
-              minus probability to die before dh-stepm .
+ #ifdef DEBUGLINMIN
-              In version up to 0.92 likelihood was computed
+     if(xxs <1.0)
-         as if date of death was unknown. Death was treated as any other
+       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 );
-         health state: the date of the interview describes the actual state
+ #endif
-         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
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   }
-         introduced the exact date of death then we should have modified
+ #ifdef DEBUGLINMIN
-         the contribution of an exact death to the likelihood. This new
+   printf("\n");
-         contribution is smaller and very dependent of the step unit
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-         stepm. It is no more the probability to die between last interview
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-         and month of death but the probability to survive from last
+   for (j=1;j<=n;j++) {
-         interview up to one month before death multiplied by the
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-         probability to die within a month. Thanks to Chris
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-         Jackson for correcting this bug.  Former versions increased
+     if(j % ncovmodel == 0){
-         mortality artificially. The bad side is that we add another loop
+       printf("\n");
-         which slows down the processing. The difference can be up to 10%
+       fprintf(ficlog,"\n");
-         lower mortality.
+     }
-           */
+   }
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ #else
+ #endif
+   free_vector(xicom,1,n);
-         } else if  (s2==-2) {
+   free_vector(pcom,1,n);
-           for (j=1,survp=0. ; j<=nlstate; j++)
+ }
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           /*survp += out[s1][j]; */
-           lli= log(survp);
+ /*************** powell ************************/
-         }
+ /*
+ Minimization of a function func of n variables. Input consists of an initial starting point
-         else if  (s2==-4) {
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-           for (j=3,survp=0. ; j<=nlstate; j++)
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-           lli= log(survp);
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-         }
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
+  */
-         else if  (s2==-5) {
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-           for (j=1,survp=0. ; j<=2; j++)
+             double (*func)(double []))
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ {
-           lli= log(survp);
+   void linmin(double p[], double xi[], int n, double *fret,
-         }
+               double (*func)(double []));
+   int i,ibig,j;
-         else{
+   double del,t,*pt,*ptt,*xit;
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+   double directest;
-           /*  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 fp,fptt;
-         }
+   double *xits;
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+   int niterf, itmp;
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+   pt=vector(1,n);
-         ipmx +=1;
+   ptt=vector(1,n);
-         sw += weight[i];
+   xit=vector(1,n);
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   xits=vector(1,n);
-       } /* end of wave */
+   *fret=(*func)(p);
-     } /* end of individual */
+   for (j=1;j<=n;j++) pt[j]=p[j];
-   }  else if(mle==2){
+   rcurr_time = time(NULL);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   for (*iter=1;;++(*iter)) {
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     fp=(*fret); /* From former iteration or initial value */
-       for(mi=1; mi<= wav[i]-1; mi++){
+     ibig=0;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     del=0.0;
-           for (j=1;j<=nlstate+ndeath;j++){
+     rlast_time=rcurr_time;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* (void) gettimeofday(&curr_time,&tzp); */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     rcurr_time = time(NULL);
-           }
+     curr_time = *localtime(&rcurr_time);
-         for(d=0; d<=dh[mi][i]; d++){
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-           newm=savm;
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-           for (kk=1; kk<=cptcovage;kk++) {
+     for (i=1;i<=n;i++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       printf(" %d %.12f",i, p[i]);
-           }
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       fprintf(ficrespow," %.12lf", p[i]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
+     printf("\n");
-           oldm=newm;
+     fprintf(ficlog,"\n");
-         } /* end mult */
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
-         s1=s[mw[mi][i]][i];
+       tml = *localtime(&rcurr_time);
-         s2=s[mw[mi+1][i]][i];
+       strcpy(strcurr,asctime(&tml));
-         bbh=(double)bh[mi][i]/(double)stepm;
+       rforecast_time=rcurr_time;
-         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 */
+       itmp = strlen(strcurr);
-         ipmx +=1;
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-         sw += weight[i];
+         strcurr[itmp-1]='\0';
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       } /* end of wave */
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-     } /* end of individual */
+       for(niterf=10;niterf<=30;niterf+=10){
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         forecast_time = *localtime(&rforecast_time);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         strcpy(strfor,asctime(&forecast_time));
-       for(mi=1; mi<= wav[i]-1; mi++){
+         itmp = strlen(strfor);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         if(strfor[itmp-1]=='\n')
-           for (j=1;j<=nlstate+ndeath;j++){
+         strfor[itmp-1]='\0';
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-           }
+       }
-         for(d=0; d<dh[mi][i]; d++){
+     }
-           newm=savm;
+     for (i=1;i<=n;i++) { /* For each direction i */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-           for (kk=1; kk<=cptcovage;kk++) {
+       fptt=(*fret);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef DEBUG
-           }
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #endif
-           savm=oldm;
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-           oldm=newm;
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-         } /* end mult */
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
+                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
-         s1=s[mw[mi][i]][i];
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-         s2=s[mw[mi+1][i]][i];
+         /* because that direction will be replaced unless the gain del is small */
-         bbh=(double)bh[mi][i]/(double)stepm;
+         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-         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 */
+         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-         ipmx +=1;
+         /* with the new direction. */
-         sw += weight[i];
+         del=fabs(fptt-(*fret));
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         ibig=i;
-       } /* end of wave */
+       }
-     } /* end of individual */
+ #ifdef DEBUG
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+       printf("%d %.12e",i,(*fret));
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (j=1;j<=n;j++) {
-       for(mi=1; mi<= wav[i]-1; mi++){
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         printf(" x(%d)=%.12e",j,xit[j]);
-           for (j=1;j<=nlstate+ndeath;j++){
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       }
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(j=1;j<=n;j++) {
-           }
+         printf(" p(%d)=%.12e",j,p[j]);
-         for(d=0; d<dh[mi][i]; d++){
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-           newm=savm;
+       }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       printf("\n");
-           for (kk=1; kk<=cptcovage;kk++) {
+       fprintf(ficlog,"\n");
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #endif
-           }
+     } /* end loop on each direction i */
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     /* New value of last point Pn is not computed, P(n-1) */
-           savm=oldm;
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-           oldm=newm;
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
-         } /* end mult */
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
-         s1=s[mw[mi][i]][i];
+       /* decreased of more than 3.84  */
-         s2=s[mw[mi+1][i]][i];
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
-         if( s2 > nlstate){
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       /* By adding 10 parameters more the gain should be 18.31 */
-         }else{
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       /* Starting the program with initial values given by a former maximization will simply change */
-         }
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-         ipmx +=1;
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
-         sw += weight[i];
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ #ifdef DEBUG
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       int k[2],l;
-       } /* end of wave */
+       k[0]=1;
-     } /* end of individual */
+       k[1]=-1;
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+       printf("Max: %.12e",(*func)(p));
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (j=1;j<=n;j++) {
-       for(mi=1; mi<= wav[i]-1; mi++){
+         printf(" %.12e",p[j]);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         fprintf(ficlog," %.12e",p[j]);
-           for (j=1;j<=nlstate+ndeath;j++){
+       }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       printf("\n");
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       fprintf(ficlog,"\n");
-           }
+       for(l=0;l<=1;l++) {
-         for(d=0; d<dh[mi][i]; d++){
+         for (j=1;j<=n;j++) {
-           newm=savm;
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-           for (kk=1; kk<=cptcovage;kk++) {
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
-           }
+         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)));
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #endif
-           savm=oldm;
-           oldm=newm;
-         } /* end mult */
+       free_vector(xit,1,n);
+       free_vector(xits,1,n);
-         s1=s[mw[mi][i]][i];
+       free_vector(ptt,1,n);
-         s2=s[mw[mi+1][i]][i];
+       free_vector(pt,1,n);
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       return;
-         ipmx +=1;
+     } /* enough precision */
-         sw += weight[i];
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+       ptt[j]=2.0*p[j]-pt[j];
-       } /* end of wave */
+       xit[j]=p[j]-pt[j];
-     } /* end of individual */
+       pt[j]=p[j];
-   } /* End of if */
+     }
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+     fptt=(*func)(ptt); /* f_3 */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ #ifdef POWELLF1F3
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ #else
-   return -l;
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
- }
+ #endif
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
- /*************** log-likelihood *************/
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
- double funcone( double *x)
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
- {
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-   /* Same as likeli but slower because of a lot of printf and if */
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-   int i, ii, j, k, mi, d, kk;
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-   double **out;
+ #ifdef NRCORIGINAL
-   double lli; /* Individual log likelihood */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-   double llt;
+ #else
-   int s1, s2;
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
-   double bbh, survp;
+       t= t- del*SQR(fp-fptt);
-   /*extern weight */
+ #endif
-   /* We are differentiating ll according to initial status */
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ #ifdef DEBUG
-   /*for(i=1;i<imx;i++)
+       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);
-     printf(" %d\n",s[4][i]);
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
-   */
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   cov[1]=1.;
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+              (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);
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       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);
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #endif
-     for(mi=1; mi<= wav[i]-1; mi++){
+ #ifdef POWELLORIGINAL
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+       if (t < 0.0) { /* Then we use it for new direction */
-         for (j=1;j<=nlstate+ndeath;j++){
+ #else
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         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);
-       for(d=0; d<dh[mi][i]; d++){
+         fprintf(ficlog,"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);
-         newm=savm;
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       }
-         for (kk=1; kk<=cptcovage;kk++) {
+       if (directest < 0.0) { /* Then we use it for new direction */
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #endif
-         }
+ #ifdef DEBUGLINMIN
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         printf("Before linmin in direction P%d-P0\n",n);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         for (j=1;j<=n;j++) {
-         savm=oldm;
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-         oldm=newm;
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-       } /* end mult */
+           if(j % ncovmodel == 0){
+             printf("\n");
-       s1=s[mw[mi][i]][i];
+             fprintf(ficlog,"\n");
-       s2=s[mw[mi+1][i]][i];
+           }
-       bbh=(double)bh[mi][i]/(double)stepm;
+         }
-       /* bias is positive if real duration
+ #endif
-        * is higher than the multiple of stepm and negative otherwise.
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-        */
+ #ifdef DEBUGLINMIN
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         for (j=1;j<=n;j++) {
-         lli=log(out[s1][s2] - savm[s1][s2]);
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-       } else if  (s2==-2) {
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-         for (j=1,survp=0. ; j<=nlstate; j++)
+           if(j % ncovmodel == 0){
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+             printf("\n");
-         lli= log(survp);
+             fprintf(ficlog,"\n");
-       }else if (mle==1){
+           }
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         }
-       } else if(mle==2){
+ #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 */
+         for (j=1;j<=n;j++) {
-       } else if(mle==3){  /* exponential inter-extrapolation */
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-         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 */
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         }
-         lli=log(out[s1][s2]); /* Original formula */
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-         lli=log(out[s1][s2]); /* Original formula */
-       } /* End of if */
+ #ifdef DEBUG
-       ipmx +=1;
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       sw += weight[i];
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         for(j=1;j<=n;j++){
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+           printf(" %.12e",xit[j]);
-       if(globpr){
+           fprintf(ficlog," %.12e",xit[j]);
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         }
-  %11.6f %11.6f %11.6f ", \
+         printf("\n");
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+         fprintf(ficlog,"\n");
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+ #endif
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+       } /* end of t or directest negative */
-           llt +=ll[k]*gipmx/gsw;
+ #ifdef POWELLF1F3
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+ #else
-         }
+     } /* end if (fptt < fp)  */
-         fprintf(ficresilk," %10.6f\n", -llt);
+ #endif
-       }
+   } /* loop iteration */
-     } /* end of wave */
+ }
-   } /* end of individual */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   /* 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 */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
-   if(globpr==0){ /* First time we count the contributions and weights */
+ {
-     gipmx=ipmx;
+   /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
-     gsw=sw;
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-   }
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-   return -l;
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
- }
+   /* or prevalence in state 1, prevalence in state 2, 0 */
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
+   /* Initial matrix pimij */
- /*************** function likelione ***********/
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
- {
+   /*  0,                   0                  , 1} */
-   /* This routine should help understanding what is done with
+   /*
-      the selection of individuals/waves and
+    * and after some iteration: */
-      to check the exact contribution to the likelihood.
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-      Plotting could be done.
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-    */
+   /*  0,                   0                  , 1} */
-   int k;
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+   /*  0.51326036147820708, 0.48673963852179264} */
-     strcpy(fileresilk,"ilk");
+   /* If we start from prlim again, prlim tends to a constant matrix */
-     strcat(fileresilk,fileres);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+   int i, ii,j,k;
-       printf("Problem with resultfile: %s\n", fileresilk);
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+   /* double **matprod2(); */ /* test */
-     }
+   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
-     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");
+   double **newm;
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+   int ncvloop=0;
-     for(k=1; k<=nlstate; k++)
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+   min=vector(1,nlstate);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   max=vector(1,nlstate);
-   }
+   meandiff=vector(1,nlstate);
-   *fretone=(*funcone)(p);
+         /* Starting with matrix unity */
-   if(*globpri !=0){
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-     fclose(ficresilk);
+     for (j=1;j<=nlstate+ndeath;j++){
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fflush(fichtm);
+     }
-   }
-   return;
+   cov[1]=1.;
- }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
- /*********** Maximum Likelihood Estimation ***************/
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     ncvloop++;
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+     newm=savm;
- {
+     /* Covariates have to be included here again */
-   int i,j, iter;
+     cov[2]=agefin;
-   double **xi;
+     if(nagesqr==1)
-   double fret;
+       cov[3]= agefin*agefin;;
-   double fretone; /* Only one call to likelihood */
+     for (k=1; k<=cptcovn;k++) {
-   /*  char filerespow[FILENAMELENGTH];*/
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-   xi=matrix(1,npar,1,npar);
+                         /* Here comes the value of the covariate 'ij' */
-   for (i=1;i<=npar;i++)
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-     for (j=1;j<=npar;j++)
+       /* 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])]); */
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+     }
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   strcpy(filerespow,"pow");
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-   strcat(filerespow,fileres);
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     for (k=1; k<=cptcovprod;k++) /* Useless */
-     printf("Problem with resultfile: %s\n", filerespow);
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-   }
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-   for (i=1;i<=nlstate;i++)
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-     for(j=1;j<=nlstate+ndeath;j++)
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   fprintf(ficrespow,"\n");
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+                 /* age and covariate values of ij are in 'cov' */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-   free_matrix(xi,1,npar,1,npar);
+     savm=oldm;
-   fclose(ficrespow);
+     oldm=newm;
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+     for(j=1; j<=nlstate; j++){
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       max[j]=0.;
+       min[j]=1.;
- }
+     }
+     for(i=1;i<=nlstate;i++){
- /**** Computes Hessian and covariance matrix ***/
+       sumnew=0;
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
- {
+       for(j=1; j<=nlstate; j++){
-   double  **a,**y,*x,pd;
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-   double **hess;
+         max[j]=FMAX(max[j],prlim[i][j]);
-   int i, j,jk;
+         min[j]=FMIN(min[j],prlim[i][j]);
-   int *indx;
+       }
+     }
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+     maxmax=0.;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+     for(j=1; j<=nlstate; j++){
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
-   double gompertz(double p[]);
+       maxmax=FMAX(maxmax,meandiff[j]);
-   hess=matrix(1,npar,1,npar);
+       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
+     } /* j loop */
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+     *ncvyear= (int)age- (int)agefin;
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
-   for (i=1;i<=npar;i++){
+     if(maxmax < ftolpl){
-     printf("%d",i);fflush(stdout);
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+       free_vector(meandiff,1,nlstate);
+       return prlim;
-     /*  printf(" %f ",p[i]);
+     }
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+   } /* 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\
-   for (i=1;i<=npar;i++) {
+ 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);
-     for (j=1;j<=npar;j++)  {
+   /* 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); */
-       if (j>i) {
+   free_vector(min,1,nlstate);
-         printf(".%d%d",i,j);fflush(stdout);
+   free_vector(max,1,nlstate);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+   free_vector(meandiff,1,nlstate);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+   return prlim; /* should not reach here */
-         hess[j][i]=hess[i][j];
+ }
-         /*printf(" %lf ",hess[i][j]);*/
-       }
-     }
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
-   }
-   printf("\n");
+  /* 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) */
-   fprintf(ficlog,"\n");
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
+  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+ {
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+   /* 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 */
-   a=matrix(1,npar,1,npar);
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-   y=matrix(1,npar,1,npar);
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-   x=vector(1,npar);
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-   indx=ivector(1,npar);
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-   for (i=1;i<=npar;i++)
+   /* Initial matrix pimij */
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-   ludcmp(a,npar,indx,&pd);
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
+   /*  0,                   0                  , 1} */
-   for (j=1;j<=npar;j++) {
+   /*
-     for (i=1;i<=npar;i++) x[i]=0;
+    * and after some iteration: */
-     x[j]=1;
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-     lubksb(a,npar,indx,x);
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-     for (i=1;i<=npar;i++){
+   /*  0,                   0                  , 1} */
-       matcov[i][j]=x[i];
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-     }
+   /* {0.51571254859325999, 0.4842874514067399, */
-   }
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
-   printf("\n#Hessian matrix#\n");
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+   int i, ii,j,k;
-   for (i=1;i<=npar;i++) {
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-     for (j=1;j<=npar;j++) {
+   /* double **matprod2(); */ /* test */
-       printf("%.3e ",hess[i][j]);
+   double **out, cov[NCOVMAX+1], **bmij();
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   double **newm;
-     }
+   double         **dnewm, **doldm, **dsavm;  /* for use */
-     printf("\n");
+   double         **oldm, **savm;  /* for use */
-     fprintf(ficlog,"\n");
-   }
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
+   int ncvloop=0;
-   /* Recompute Inverse */
-   for (i=1;i<=npar;i++)
+   min=vector(1,nlstate);
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   max=vector(1,nlstate);
-   ludcmp(a,npar,indx,&pd);
+   meandiff=vector(1,nlstate);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+         oldm=oldms; savm=savms;
-   for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
+         /* Starting with matrix unity */
-     x[j]=1;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     lubksb(a,npar,indx,x);
+                 for (j=1;j<=nlstate+ndeath;j++){
-     for (i=1;i<=npar;i++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       y[i][j]=x[i];
+     }
-       printf("%.3e ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   cov[1]=1.;
-     }
-     printf("\n");
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-     fprintf(ficlog,"\n");
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-   }
+   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-   */
+   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+     ncvloop++;
-   free_matrix(a,1,npar,1,npar);
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
-   free_matrix(y,1,npar,1,npar);
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
-   free_vector(x,1,npar);
+     /* Covariates have to be included here again */
-   free_ivector(indx,1,npar);
+     cov[2]=agefin;
-   free_matrix(hess,1,npar,1,npar);
+     if(nagesqr==1)
+       cov[3]= agefin*agefin;;
+     for (k=1; k<=cptcovn;k++) {
- }
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
- /*************** hessian matrix ****************/
+       /* 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])]); */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+     }
- {
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   int i;
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-   int l=1, lmax=20;
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
-   double k1,k2;
+     for (k=1; k<=cptcovprod;k++) /* Useless */
-   double p2[NPARMAX+1];
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-   double res;
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-   int k=0,kmax=10;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-   double l1;
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   fx=func(x);
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+                 /* ij should be linked to the correct index of cov */
-   for(l=0 ; l <=lmax; l++){
+                 /* age and covariate values ij are in 'cov', but we need to pass
-     l1=pow(10,l);
+                  * ij for the observed prevalence at age and status and covariate
-     delts=delt;
+                  * number:  prevacurrent[(int)agefin][ii][ij]
-     for(k=1 ; k <kmax; k=k+1){
+                  */
-       delt = delta*(l1*k);
+     /* 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 *\/ */
-       p2[theta]=x[theta] +delt;
+     /* 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 *\/ */
-       k1=func(p2)-fx;
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
-       p2[theta]=x[theta]-delt;
+     savm=oldm;
-       k2=func(p2)-fx;
+     oldm=newm;
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+     for(j=1; j<=nlstate; j++){
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+       max[j]=0.;
+       min[j]=1.;
- #ifdef DEBUG
+     }
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+     for(j=1; j<=nlstate; j++){
-       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);
+       for(i=1;i<=nlstate;i++){
- #endif
+                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+                                 bprlim[i][j]= newm[i][j];
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
-         k=kmax;
+                                 min[i]=FMIN(min[i],bprlim[i][j]);
        }
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+     }
-         k=kmax; l=lmax*10.;
-       }
+     maxmax=0.;
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+     for(i=1; i<=nlstate; i++){
-         delts=delt;
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
-       }
+       maxmax=FMAX(maxmax,meandiff[i]);
-     }
+       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
-   }
+     } /* j loop */
-   delti[theta]=delts;
+     *ncvyear= -( (int)age- (int)agefin);
-   return res;
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
+     if(maxmax < ftolpl){
- }
+       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+       free_vector(max,1,nlstate);
- {
+       free_vector(meandiff,1,nlstate);
-   int i;
+       return bprlim;
-   int l=1, l1, lmax=20;
+     }
-   double k1,k2,k3,k4,res,fx;
+   } /* age loop */
-   double p2[NPARMAX+1];
+     /* After some age loop it doesn't converge */
-   int k;
+   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\
+ 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);
-   fx=func(x);
+   /* 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); */
-   for (k=1; k<=2; k++) {
+   free_vector(min,1,nlstate);
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+   free_vector(max,1,nlstate);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   free_vector(meandiff,1,nlstate);
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-     k1=func(p2)-fx;
+   return bprlim; /* should not reach here */
+ }
-     p2[thetai]=x[thetai]+delti[thetai]/k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ /*************** transition probabilities ***************/
-     k2=func(p2)-fx;
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+ {
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-     k3=func(p2)-fx;
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-     k4=func(p2)-fx;
+      ncth covariate in the global vector x is given by the formula:
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
- #ifdef DEBUG
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-     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);
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-     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);
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
- #endif
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-   }
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-   return res;
+   */
- }
+   double s1, lnpijopii;
+   /*double t34;*/
- /************** Inverse of matrix **************/
+   int i,j, nc, ii, jj;
- void ludcmp(double **a, int n, int *indx, double *d)
- {
+         for(i=1; i<= nlstate; i++){
-   int i,imax,j,k;
+                 for(j=1; j<i;j++){
-   double big,dum,sum,temp;
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   double *vv;
+                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
+                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-   vv=vector(1,n);
+                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   *d=1.0;
+                         }
-   for (i=1;i<=n;i++) {
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-     big=0.0;
+                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     for (j=1;j<=n;j++)
+                 }
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+                 for(j=i+1; j<=nlstate+ndeath;j++){
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-     vv[i]=1.0/big;
+                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-   }
+                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-   for (j=1;j<=n;j++) {
+                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-     for (i=1;i<j;i++) {
+                         }
-       sum=a[i][j];
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+                 }
-       a[i][j]=sum;
+         }
-     }
-     big=0.0;
+         for(i=1; i<= nlstate; i++){
-     for (i=j;i<=n;i++) {
+                 s1=0;
-       sum=a[i][j];
+                 for(j=1; j<i; j++){
-       for (k=1;k<j;k++)
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         sum -= a[i][k]*a[k][j];
+                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       a[i][j]=sum;
+                 }
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+                 for(j=i+1; j<=nlstate+ndeath; j++){
-         big=dum;
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         imax=i;
+                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       }
+                 }
-     }
+                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-     if (j != imax) {
+                 ps[i][i]=1./(s1+1.);
-       for (k=1;k<=n;k++) {
+                 /* Computing other pijs */
-         dum=a[imax][k];
+                 for(j=1; j<i; j++)
-         a[imax][k]=a[j][k];
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         a[j][k]=dum;
+                 for(j=i+1; j<=nlstate+ndeath; j++)
-       }
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       *d = -(*d);
+                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-       vv[imax]=vv[j];
+         } /* end i */
-     }
-     indx[j]=imax;
+         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+                 for(jj=1; jj<= nlstate+ndeath; jj++){
-     if (j != n) {
+                         ps[ii][jj]=0;
-       dum=1.0/(a[j][j]);
+                         ps[ii][ii]=1;
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+                 }
-     }
+         }
-   }
-   free_vector(vv,1,n);  /* Doesn't work */
- ;
+         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
- }
+         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
- void lubksb(double **a, int n, int *indx, double b[])
+         /*   } */
- {
+         /*   printf("\n "); */
-   int i,ii=0,ip,j;
+         /* } */
-   double sum;
+         /* printf("\n ");printf("%lf ",cov[2]);*/
+         /*
-   for (i=1;i<=n;i++) {
+                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
-     ip=indx[i];
+                 goto end;*/
-     sum=b[ip];
+         return ps;
-     b[ip]=b[i];
+ }
-     if (ii)
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+ /*************** backward transition probabilities ***************/
-     else if (sum) ii=i;
-     b[i]=sum;
+  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-   }
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-   for (i=n;i>=1;i--) {
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
-     sum=b[i];
+ {
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+         /* Computes the backward probability at age agefin and covariate ij
-     b[i]=sum/a[i][i];
+          * and returns in **ps as well as **bmij.
-   }
+          */
- }
+   int i, ii, j,k;
- void pstamp(FILE *fichier)
+         double **out, **pmij();
- {
+         double sumnew=0.;
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   double agefin;
- }
+         double **dnewm, **dsavm, **doldm;
- /************ Frequencies ********************/
+         double **bbmij;
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
- {  /* Some frequencies */
+   doldm=ddoldms; /* global pointers */
+         dnewm=ddnewms;
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+         dsavm=ddsavms;
-   int first;
-   double ***freq; /* Frequencies */
+         agefin=cov[2];
-   double *pp, **prop;
+         /* bmij *//* age is cov[2], ij is included in cov, but we need for
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+                  the observed prevalence (with this covariate ij) */
-   char fileresp[FILENAMELENGTH];
+         dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+         /* We do have the matrix Px in savm  and we need pij */
-   pp=vector(1,nlstate);
+         for (j=1;j<=nlstate+ndeath;j++){
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+                 sumnew=0.; /* w1 p11 + w2 p21 only on live states */
-   strcpy(fileresp,"p");
+                 for (ii=1;ii<=nlstate;ii++){
-   strcat(fileresp,fileres);
+                         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+                 } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+                 for (ii=1;ii<=nlstate+ndeath;ii++){
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+                         if(sumnew >= 1.e-10){
-     exit(0);
+                                 /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
-   }
+                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+                                 /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
-   j1=0;
+                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+                                 /* }else */
-   j=cptcoveff;
+                                         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+                         }else{
+                                 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);
-   first=1;
+                         }
+                 } /*End ii */
-   for(k1=1; k1<=j;k1++){
+         } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+                 /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
-       j1++;
+         bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
-         scanf("%d", i);*/
+         /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-       for (i=-5; i<=nlstate+ndeath; i++)
+         /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+         /* left Product of this matrix by diag matrix of prevalences (savm) */
-           for(m=iagemin; m <= iagemax+3; m++)
+         for (j=1;j<=nlstate+ndeath;j++){
-             freq[i][jk][m]=0;
+                 for (ii=1;ii<=nlstate+ndeath;ii++){
+                         dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
-     for (i=1; i<=nlstate; i++)
+                 }
-       for(m=iagemin; m <= iagemax+3; m++)
+         } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
-         prop[i][m]=0;
+         ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
+         /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
-       dateintsum=0;
+         /* end bmij */
-       k2cpt=0;
+         return ps;
-       for (i=1; i<=imx; i++) {
+ }
-         bool=1;
+ /*************** transition probabilities ***************/
-         if  (cptcovn>0) {
-           for (z1=1; z1<=cptcoveff; z1++)
+ double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+ {
-               bool=0;
+   /* 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
-         if (bool==1){
+      model to the ncovmodel covariates (including constant and age).
-           for(m=firstpass; m<=lastpass; m++){
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-             k2=anint[m][i]+(mint[m][i]/12.);
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+      ncth covariate in the global vector x is given by the formula:
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-               if (m<lastpass) {
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-               }
+   */
+   double s1, lnpijopii;
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+   /*double t34;*/
-                 dateintsum=dateintsum+k2;
+   int i,j, nc, ii, jj;
-                 k2cpt++;
-               }
+         for(i=1; i<= nlstate; i++){
-               /*}*/
+                 for(j=1; j<i;j++){
-           }
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         }
+                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
-       }
+                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+                         }
-       pstamp(ficresp);
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       if  (cptcovn>0) {
+                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         fprintf(ficresp, "\n#********** Variable ");
+                 }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+                 for(j=i+1; j<=nlstate+ndeath;j++){
-         fprintf(ficresp, "**********\n#");
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-       }
+                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-       for(i=1; i<=nlstate;i++)
+                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-       fprintf(ficresp, "\n");
+                         }
+                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       for(i=iagemin; i <= iagemax+3; i++){
+                 }
-         if(i==iagemax+3){
+         }
-           fprintf(ficlog,"Total");
-         }else{
+         for(i=1; i<= nlstate; i++){
-           if(first==1){
+                 s1=0;
-             first=0;
+                 for(j=1; j<i; j++){
-             printf("See log file for details...\n");
+                         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); */
-           fprintf(ficlog,"Age %d", i);
+                 }
-         }
+                 for(j=i+1; j<=nlstate+ndeath; j++){
-         for(jk=1; jk <=nlstate ; jk++){
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-             pp[jk] += freq[jk][m][i];
+                 }
-         }
+                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         for(jk=1; jk <=nlstate ; jk++){
+                 ps[i][i]=1./(s1+1.);
-           for(m=-1, pos=0; m <=0 ; m++)
+                 /* Computing other pijs */
-             pos += freq[jk][m][i];
+                 for(j=1; j<i; j++)
-           if(pp[jk]>=1.e-10){
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-             if(first==1){
+                 for(j=i+1; j<=nlstate+ndeath; j++)
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                         ps[i][j]= exp(ps[i][j])*ps[i][i];
-             }
+                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         } /* end i */
-           }else{
-             if(first==1)
+         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                 for(jj=1; jj<= nlstate+ndeath; jj++){
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                         ps[ii][jj]=0;
-           }
+                         ps[ii][ii]=1;
-         }
+                 }
+         }
-         for(jk=1; jk <=nlstate ; jk++){
+         /* Added for backcast */ /* Transposed matrix too */
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+         for(jj=1; jj<= nlstate+ndeath; jj++){
-             pp[jk] += freq[jk][m][i];
+                 s1=0.;
-         }
+                 for(ii=1; ii<= nlstate+ndeath; ii++){
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+                         s1+=ps[ii][jj];
-           pos += pp[jk];
+                 }
-           posprop += prop[jk][i];
+                 for(ii=1; ii<= nlstate; ii++){
-         }
+                         ps[ii][jj]=ps[ii][jj]/s1;
-         for(jk=1; jk <=nlstate ; jk++){
+                 }
-           if(pos>=1.e-5){
+         }
-             if(first==1)
+         /* Transposition */
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         for(jj=1; jj<= nlstate+ndeath; jj++){
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                 for(ii=jj; ii<= nlstate+ndeath; ii++){
-           }else{
+                         s1=ps[ii][jj];
-             if(first==1)
+                         ps[ii][jj]=ps[jj][ii];
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                         ps[jj][ii]=s1;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                 }
-           }
+         }
-           if( i <= iagemax){
+         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-             if(pos>=1.e-5){
+         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+         /*   } */
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+         /*   printf("\n "); */
-             }
+         /* } */
-             else
+         /* printf("\n ");printf("%lf ",cov[2]);*/
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+         /*
-           }
+                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
-         }
+                 goto end;*/
+         return ps;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+ }
-           for(m=-1; m <=nlstate+ndeath; m++)
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+ /**************** Product of 2 matrices ******************/
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-             }
+ {
-         if(i <= iagemax)
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-           fprintf(ficresp,"\n");
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         if(first==1)
+   /* in, b, out are matrice of pointers which should have been initialized
-           printf("Others in log...\n");
+      before: only the contents of out is modified. The function returns
-         fprintf(ficlog,"\n");
+      a pointer to pointers identical to out */
-       }
+   int i, j, k;
-     }
+   for(i=nrl; i<= nrh; i++)
-   }
+     for(k=ncolol; k<=ncoloh; k++){
-   dateintmean=dateintsum/k2cpt;
+       out[i][k]=0.;
+       for(j=ncl; j<=nch; j++)
-   fclose(ficresp);
+         out[i][k] +=in[i][j]*b[j][k];
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+     }
-   free_vector(pp,1,nlstate);
+   return out;
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+ }
-   /* End of Freq */
- }
+ /************* Higher Matrix Product ***************/
- /************ Prevalence ********************/
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  {
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      'nhstepm*hstepm*stepm' months (i.e. until
-      We still use firstpass and lastpass as another selection.
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   */
+      nhstepm*hstepm matrices.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+      (typically every 2 years instead of every month which is too big
-   double ***freq; /* Frequencies */
+      for the memory).
-   double *pp, **prop;
+      Model is determined by parameters x and covariates have to be
-   double pos,posprop;
+      included manually here.
-   double  y2; /* in fractional years */
-   int iagemin, iagemax;
+      */
-   iagemin= (int) agemin;
+   int i, j, d, h, k;
-   iagemax= (int) agemax;
+   double **out, cov[NCOVMAX+1];
-   /*pp=vector(1,nlstate);*/
+   double **newm;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   double agexact;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+   double agebegin, ageend;
-   j1=0;
+   /* Hstepm could be zero and should return the unit matrix */
-   j=cptcoveff;
+   for (i=1;i<=nlstate+ndeath;i++)
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-   for(k1=1; k1<=j;k1++){
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     }
-       j1++;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
-       for (i=1; i<=nlstate; i++)
+     for(d=1; d <=hstepm; d++){
-         for(m=iagemin; m <= iagemax+3; m++)
+       newm=savm;
-           prop[i][m]=0.0;
+       /* Covariates have to be included here again */
+       cov[1]=1.;
-       for (i=1; i<=imx; i++) { /* Each individual */
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-         bool=1;
+       cov[2]=agexact;
-         if  (cptcovn>0) {
+       if(nagesqr==1)
-           for (z1=1; z1<=cptcoveff; z1++)
+                                 cov[3]= agexact*agexact;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+       for (k=1; k<=cptcovn;k++)
-               bool=0;
+                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-         }
+                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-         if (bool==1) {
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+                                 cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-               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);
+                         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-                 prop[s[m][i]][iagemax+3] += weight[i];
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-               }
+                         /* right multiplication of oldm by the current matrix */
-             }
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-           } /* end selection of waves */
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-         }
+       /* if((int)age == 70){ */
-       }
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
-       for(i=iagemin; i <= iagemax+3; i++){
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-           posprop += prop[jk][i];
+       /*            printf("%f ",pmmij[i][j]); */
-         }
+       /*          } */
+       /*          printf(" oldm "); */
-         for(jk=1; jk <=nlstate ; jk++){
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-           if( i <=  iagemax){
+       /*            printf("%f ",oldm[i][j]); */
-             if(posprop>=1.e-5){
+       /*          } */
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+       /*          printf("\n"); */
-             }
+       /*        } */
-           }
+       /* } */
-         }/* end jk */
+       savm=oldm;
-       }/* end i */
+       oldm=newm;
-     } /* end i1 */
+     }
-   } /* end k1 */
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+                                 po[i][j][h]=newm[i][j];
-   /*free_vector(pp,1,nlstate);*/
+                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+       }
- }  /* End of prevalence */
+     /*printf("h=%d ",h);*/
+   } /* end h */
- /************* Waves Concatenation ***************/
+         /*     printf("\n H=%d \n",h); */
+   return po;
- void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+ }
- {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+ /************* Higher Back Matrix Product ***************/
-      Death is a valid wave (if date is known).
+ /* 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 ) */
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
-      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.
+   /* 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
-   int i, mi, m;
+      nhstepm*hstepm matrices.
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-      double sum=0., jmean=0.;*/
+      (typically every 2 years instead of every month which is too big
-   int first;
+      for the memory).
-   int j, k=0,jk, ju, jl;
+      Model is determined by parameters x and covariates have to be
-   double sum=0.;
+      included manually here.
-   first=0;
-   jmin=1e+5;
+      */
-   jmax=-1;
-   jmean=0.;
+   int i, j, d, h, k;
-   for(i=1; i<=imx; i++){
+   double **out, cov[NCOVMAX+1];
-     mi=0;
+   double **newm;
-     m=firstpass;
+   double agexact;
-     while(s[m][i] <= nlstate){
+   double agebegin, ageend;
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+         double **oldm, **savm;
-         mw[++mi][i]=m;
-       if(m >=lastpass)
+         oldm=oldms;savm=savms;
-         break;
+   /* Hstepm could be zero and should return the unit matrix */
-       else
+   for (i=1;i<=nlstate+ndeath;i++)
-         m++;
+     for (j=1;j<=nlstate+ndeath;j++){
-     }/* end while */
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-     if (s[m][i] > nlstate){
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-       mi++;     /* Death is another wave */
+     }
-       /* if(mi==0)  never been interviewed correctly before death */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-          /* Only death is a correct wave */
+   for(h=1; h <=nhstepm; h++){
-       mw[mi][i]=m;
+     for(d=1; d <=hstepm; d++){
-     }
+       newm=savm;
+       /* Covariates have to be included here again */
-     wav[i]=mi;
+       cov[1]=1.;
-     if(mi==0){
+       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-       nbwarn++;
+       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
-       if(first==0){
+       cov[2]=agexact;
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+       if(nagesqr==1)
-         first=1;
+                                 cov[3]= agexact*agexact;
-       }
+       for (k=1; k<=cptcovn;k++)
-       if(first==1){
+                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-       }
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-     } /* end mi==0 */
+                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   } /* End individuals */
+                                 cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
-   for(i=1; i<=imx; i++){
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-     for(mi=1; mi<wav[i];mi++){
+                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-       if (stepm <=0)
+                         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-         dh[mi][i]=1;
-       else{
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-           if (agedc[i] < 2*AGESUP) {
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+       /* Careful transposed matrix */
-             if(j==0) j=1;  /* Survives at least one month after exam */
+                         /* age is in cov[2] */
-             else if(j<0){
+       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
-               nberr++;
+                         /*                                               1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
-               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]);
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
-               j=1; /* Temporary Dangerous patch */
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-               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);
+       /* if((int)age == 70){ */
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
-               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);
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
-             }
+       /*          printf("%d pmmij ",i); */
-             k=k+1;
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-             if (j >= jmax){
+       /*            printf("%f ",pmmij[i][j]); */
-               jmax=j;
+       /*          } */
-               ijmax=i;
+       /*          printf(" oldm "); */
-             }
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
-             if (j <= jmin){
+       /*            printf("%f ",oldm[i][j]); */
-               jmin=j;
+       /*          } */
-               ijmin=i;
+       /*          printf("\n"); */
-             }
+       /*        } */
-             sum=sum+j;
+       /* } */
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+       savm=oldm;
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+       oldm=newm;
-           }
+     }
-         }
+     for(i=1; i<=nlstate+ndeath; i++)
-         else{
+       for(j=1;j<=nlstate+ndeath;j++) {
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+                                 po[i][j][h]=newm[i][j];
- /*        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]); */
+                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
-           k=k+1;
+     /*printf("h=%d ",h);*/
-           if (j >= jmax) {
+   } /* end h */
-             jmax=j;
+         /*     printf("\n H=%d \n",h); */
-             ijmax=i;
+   return po;
-           }
+ }
-           else if (j <= jmin){
-             jmin=j;
-             ijmin=i;
+ #ifdef NLOPT
-           }
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   double fret;
-           /*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]);*/
+   double *xt;
-           if(j<0){
+   int j;
-             nberr++;
+   myfunc_data *d2 = (myfunc_data *) pd;
-             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]);
+ /* xt = (p1-1); */
-             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]);
+   xt=vector(1,n);
-           }
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-           sum=sum+j;
-         }
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-         jk= j/stepm;
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-         jl= j -jk*stepm;
+   printf("Function = %.12lf ",fret);
-         ju= j -(jk+1)*stepm;
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   printf("\n");
-           if(jl==0){
+  free_vector(xt,1,n);
-             dh[mi][i]=jk;
+   return fret;
-             bh[mi][i]=0;
+ }
-           }else{ /* We want a negative bias in order to only have interpolation ie
+ #endif
-                   * at the price of an extra matrix product in likelihood */
-             dh[mi][i]=jk+1;
+ /*************** log-likelihood *************/
-             bh[mi][i]=ju;
+ double func( double *x)
-           }
+ {
-         }else{
+   int i, ii, j, k, mi, d, kk;
-           if(jl <= -ju){
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-             dh[mi][i]=jk;
+   double **out;
-             bh[mi][i]=jl;       /* bias is positive if real duration
+   double sw; /* Sum of weights */
-                                  * is higher than the multiple of stepm and negative otherwise.
+   double lli; /* Individual log likelihood */
-                                  */
+   int s1, s2;
-           }
+   double bbh, survp;
-           else{
+   long ipmx;
-             dh[mi][i]=jk+1;
+   double agexact;
-             bh[mi][i]=ju;
+   /*extern weight */
-           }
+   /* We are differentiating ll according to initial status */
-           if(dh[mi][i]==0){
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-             dh[mi][i]=1; /* At least one step */
+   /*for(i=1;i<imx;i++)
-             bh[mi][i]=ju; /* At least one step */
+     printf(" %d\n",s[4][i]);
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+   */
-           }
-         } /* end if mle */
+   ++countcallfunc;
-       }
-     } /* end wave */
+   cov[1]=1.;
-   }
-   jmean=sum/k;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+   if(mle==1){
-  }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* Computes the values of the ncovmodel covariates of the model
- /*********** Tricode ****************************/
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
- void tricode(int *Tvar, int **nbcode, int imx)
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
- {
+          to be observed in j being in i according to the model.
+        */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-   int cptcode=0;
+           cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   cptcoveff=0;
+       }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+          has been calculated etc */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+           for (j=1;j<=nlstate+ndeath;j++){
-                                modality*/
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       Ndum[ij]++; /*store the modality */
+           }
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+         for(d=0; d<dh[mi][i]; d++){
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+           newm=savm;
-                                        Tvar[j]. If V=sex and male is 0 and
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-                                        female is 1, then  cptcode=1.*/
+           cov[2]=agexact;
-     }
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-     for (i=0; i<=cptcode; i++) {
+           for (kk=1; kk<=cptcovage;kk++) {
-       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 */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-     }
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     ij=1;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for (i=1; i<=ncodemax[j]; i++) {
+           savm=oldm;
-       for (k=0; k<= maxncov; k++) {
+           oldm=newm;
-         if (Ndum[k] != 0) {
+         } /* end mult */
-           nbcode[Tvar[j]][ij]=k;
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+         /*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.
-           ij++;
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         }
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         if (ij > ncodemax[j]) break;
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-       }
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-     }
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-   }
+          * probability in order to take into account the bias as a fraction of the way
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+          * -stepm/2 to stepm/2 .
+          * For stepm=1 the results are the same as for previous versions of Imach.
-  for (i=1; i<=ncovmodel-2; i++) {
+          * For stepm > 1 the results are less biased than in previous versions.
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+          */
-    ij=Tvar[i];
+         s1=s[mw[mi][i]][i];
-    Ndum[ij]++;
+         s2=s[mw[mi+1][i]][i];
-  }
+         bbh=(double)bh[mi][i]/(double)stepm;
+         /* bias bh is positive if real duration
-  ij=1;
+          * is higher than the multiple of stepm and negative otherwise.
-  for (i=1; i<= maxncov; i++) {
+          */
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-      Tvaraff[ij]=i; /*For printing */
+         if( s2 > nlstate){
-      ij++;
+           /* i.e. if s2 is a death state and if the date of death is known
-    }
+              then the contribution to the likelihood is the probability to
-  }
+              die between last step unit time and current  step unit time,
+              which is also equal to probability to die before dh
-  cptcoveff=ij-1; /*Number of simple covariates*/
+              minus probability to die before dh-stepm .
- }
+              In version up to 0.92 likelihood was computed
+         as if date of death was unknown. Death was treated as any other
- /*********** Health Expectancies ****************/
+         health state: the date of the interview describes the actual state
+         and not the date of a change in health state. The former idea was
- 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[] )
+         to consider that at each interview the state was recorded
+         (healthy, disable or death) and IMaCh was corrected; but when we
- {
+         introduced the exact date of death then we should have modified
-   /* Health expectancies, no variances */
+         the contribution of an exact death to the likelihood. This new
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+         contribution is smaller and very dependent of the step unit
-   double age, agelim, hf;
+         stepm. It is no more the probability to die between last interview
-   double ***p3mat;
+         and month of death but the probability to survive from last
-   double eip;
+         interview up to one month before death multiplied by the
+         probability to die within a month. Thanks to Chris
-   pstamp(ficreseij);
+         Jackson for correcting this bug.  Former versions increased
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+         mortality artificially. The bad side is that we add another loop
-   fprintf(ficreseij,"# Age");
+         which slows down the processing. The difference can be up to 10%
-   for(i=1; i<=nlstate;i++){
+         lower mortality.
-     for(j=1; j<=nlstate;j++){
+           */
-       fprintf(ficreseij," e%1d%1d ",i,j);
+         /* If, at the beginning of the maximization mostly, the
-     }
+            cumulative probability or probability to be dead is
-     fprintf(ficreseij," e%1d. ",i);
+            constant (ie = 1) over time d, the difference is equal to
-   }
+.  out[s1][3] = savm[s1][3]: probability, being at state
-   fprintf(ficreseij,"\n");
+            s1 at precedent wave, to be dead a month before current
+            wave is equal to probability, being at state s1 at
+            precedent wave, to be dead at mont of the current
-   if(estepm < stepm){
+            wave. Then the observed probability (that this person died)
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+            is null according to current estimated parameter. In fact,
-   }
+            it should be very low but not zero otherwise the log go to
-   else  hstepm=estepm;
+            infinity.
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+         */
-    * This is mainly to measure the difference between two models: for example
+ /* #ifdef INFINITYORIGINAL */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+ /* #else */
-    * progression in between and thus overestimating or underestimating according
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-    * to the curvature of the survival function. If, for the same date, we
+ /*          lli=log(mytinydouble); */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ /*        else */
-    * to compare the new estimate of Life expectancy with the same linear
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-    * hypothesis. A more precise result, taking into account a more precise
+ /* #endif */
-    * curvature will be obtained if estepm is as small as stepm. */
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+         } else if  ( s2==-1 ) { /* alive */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+           for (j=1,survp=0. ; j<=nlstate; j++)
-      nhstepm is the number of hstepm from age to agelim
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-      nstepm is the number of stepm from age to agelin.
+           /*survp += out[s1][j]; */
-      Look at hpijx to understand the reason of that which relies in memory size
+           lli= log(survp);
-      and note for a fixed period like estepm months */
+         }
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+         else if  (s2==-4) {
-      survival function given by stepm (the optimization length). Unfortunately it
+           for (j=3,survp=0. ; j<=nlstate; j++)
-      means that if the survival funtion is printed only each two years of age and if
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+           lli= log(survp);
-      results. So we changed our mind and took the option of the best precision.
+         }
-   */
+         else if  (s2==-5) {
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   agelim=AGESUP;
+           lli= log(survp);
-   /* If stepm=6 months */
+         }
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+         else{
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
- /* nhstepm age range expressed in number of stepm */
+         }
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         /*if(lli ==000.0)*/
-   /* if (stepm >= YEARM) hstepm=1;*/
+         /*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); */
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         ipmx +=1;
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   for (age=bage; age<=fage; age ++){
+         /* if (lli < log(mytinydouble)){ */
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+         /* } */
+       } /* end of wave */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     } /* end of individual */
+   }  else if(mle==2){
-     printf("%d|",(int)age);fflush(stdout);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     /* Computing expectancies */
+           for (j=1;j<=nlstate+ndeath;j++){
-     for(i=1; i<=nlstate;i++)
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(j=1; j<=nlstate;j++)
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         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;
+         for(d=0; d<=dh[mi][i]; d++){
+           newm=savm;
-           /*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]);*/
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
-         }
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-     fprintf(ficreseij,"%3.0f",age );
+           for (kk=1; kk<=cptcovage;kk++) {
-     for(i=1; i<=nlstate;i++){
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-       eip=0;
+           }
-       for(j=1; j<=nlstate;j++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         eip +=eij[i][j][(int)age];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+           savm=oldm;
-       }
+           oldm=newm;
-       fprintf(ficreseij,"%9.4f", eip );
+         } /* end mult */
-     }
-     fprintf(ficreseij,"\n");
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   }
+         bbh=(double)bh[mi][i]/(double)stepm;
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   printf("\n");
+         ipmx +=1;
-   fprintf(ficlog,"\n");
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- }
+       } /* end of wave */
+     } /* end of individual */
- 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[] )
+   }  else if(mle==3){  /* exponential inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- {
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   /* Covariances of health expectancies eij and of total life expectancies according
+       for(mi=1; mi<= wav[i]-1; mi++){
-    to initial status i, ei. .
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   */
+           for (j=1;j<=nlstate+ndeath;j++){
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double age, agelim, hf;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double ***p3matp, ***p3matm, ***varhe;
+           }
-   double **dnewm,**doldm;
+         for(d=0; d<dh[mi][i]; d++){
-   double *xp, *xm;
+           newm=savm;
-   double **gp, **gm;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   double ***gradg, ***trgradg;
+           cov[2]=agexact;
-   int theta;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-   double eip, vip;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+           }
-   xp=vector(1,npar);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   xm=vector(1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+           savm=oldm;
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+           oldm=newm;
+         } /* end mult */
-   pstamp(ficresstdeij);
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+         s1=s[mw[mi][i]][i];
-   fprintf(ficresstdeij,"# Age");
+         s2=s[mw[mi+1][i]][i];
-   for(i=1; i<=nlstate;i++){
+         bbh=(double)bh[mi][i]/(double)stepm;
-     for(j=1; j<=nlstate;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 */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+         ipmx +=1;
-     fprintf(ficresstdeij," e%1d. ",i);
+         sw += weight[i];
-   }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   fprintf(ficresstdeij,"\n");
+       } /* end of wave */
+     } /* end of individual */
-   pstamp(ficrescveij);
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficrescveij,"# Age");
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   for(i=1; i<=nlstate;i++)
+       for(mi=1; mi<= wav[i]-1; mi++){
-     for(j=1; j<=nlstate;j++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       cptj= (j-1)*nlstate+i;
+           for (j=1;j<=nlstate+ndeath;j++){
-       for(i2=1; i2<=nlstate;i2++)
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for(j2=1; j2<=nlstate;j2++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           cptj2= (j2-1)*nlstate+i2;
+           }
-           if(cptj2 <= cptj)
+         for(d=0; d<dh[mi][i]; d++){
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+           newm=savm;
-         }
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     }
+           cov[2]=agexact;
-   fprintf(ficrescveij,"\n");
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
-   if(estepm < stepm){
+           for (kk=1; kk<=cptcovage;kk++) {
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   }
+           }
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-    * This is mainly to measure the difference between two models: for example
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+           savm=oldm;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+           oldm=newm;
-    * progression in between and thus overestimating or underestimating according
+         } /* end mult */
-    * 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
+         s1=s[mw[mi][i]][i];
-    * to compare the new estimate of Life expectancy with the same linear
+         s2=s[mw[mi+1][i]][i];
-    * hypothesis. A more precise result, taking into account a more precise
+         if( s2 > nlstate){
-    * curvature will be obtained if estepm is as small as stepm. */
+           lli=log(out[s1][s2] - savm[s1][s2]);
+         } 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 estepm months */
+         }
-   /* 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 only each 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 */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   /* If stepm=6 months */
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   /* nhstepm age range expressed in number of stepm */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   agelim=AGESUP;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+           for (j=1;j<=nlstate+ndeath;j++){
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /* if (stepm >= YEARM) hstepm=1;*/
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+           }
+         for(d=0; d<dh[mi][i]; d++){
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           newm=savm;
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+           cov[2]=agexact;
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+           if(nagesqr==1)
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+             cov[3]= agexact*agexact;
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   for (age=bage; age<=fage; age ++){
+           }
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           oldm=newm;
+         } /* end mult */
-     /* Computing  Variances of health expectancies */
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+         s1=s[mw[mi][i]][i];
-        decrease memory allocation */
+         s2=s[mw[mi+1][i]][i];
-     for(theta=1; theta <=npar; theta++){
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       for(i=1; i<=npar; i++){
+         ipmx +=1;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         sw += weight[i];
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       }
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       } /* end of wave */
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+     } /* end of individual */
+   } /* End of if */
-       for(j=1; j<= nlstate; j++){
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-         for(i=1; i<=nlstate; i++){
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-           for(h=0; h<=nhstepm-1; h++){
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+   return -l;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+ }
-           }
-         }
+ /*************** log-likelihood *************/
-       }
+ double funcone( double *x)
+ {
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+   /* Same as likeli but slower because of a lot of printf and if */
-         for(h=0; h<=nhstepm-1; h++){
+   int i, ii, j, k, mi, d, kk;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-         }
+   double **out;
-     }/* End theta */
+   double lli; /* Individual log likelihood */
+   double llt;
+   int s1, s2;
-     for(h=0; h<=nhstepm-1; h++)
+   double bbh, survp;
-       for(j=1; j<=nlstate*nlstate;j++)
+   double agexact;
-         for(theta=1; theta <=npar; theta++)
+   double agebegin, ageend;
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   /*for(i=1;i<imx;i++)
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+     printf(" %d\n",s[4][i]);
-         varhe[ij][ji][(int)age] =0.;
+   */
+   cov[1]=1.;
-      printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-      for(h=0;h<=nhstepm-1;h++){
-       for(k=0;k<=nhstepm-1;k++){
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+     for(mi=1; mi<= wav[i]-1; mi++){
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+         for (j=1;j<=nlstate+ndeath;j++){
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       }
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     }
+         }
-     /* Computing expectancies */
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
-     for(i=1; i<=nlstate;i++)
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-       for(j=1; j<=nlstate;j++)
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           and mw[mi+1][i]. dh depends on stepm.*/
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+         newm=savm;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         cov[2]=agexact;
+         if(nagesqr==1)
-         }
+           cov[3]= agexact*agexact;
+         for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(ficresstdeij,"%3.0f",age );
+           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-     for(i=1; i<=nlstate;i++){
+         }
-       eip=0.;
-       vip=0.;
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-       for(j=1; j<=nlstate;j++){
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         eip += eij[i][j][(int)age];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+         savm=oldm;
-       }
+         oldm=newm;
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+       } /* end mult */
-     }
-     fprintf(ficresstdeij,"\n");
+       s1=s[mw[mi][i]][i];
+       s2=s[mw[mi+1][i]][i];
-     fprintf(ficrescveij,"%3.0f",age );
+       /* if(s2==-1){ */
-     for(i=1; i<=nlstate;i++)
+       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
-       for(j=1; j<=nlstate;j++){
+       /*        /\* exit(1); *\/ */
-         cptj= (j-1)*nlstate+i;
+       /* } */
-         for(i2=1; i2<=nlstate;i2++)
+       bbh=(double)bh[mi][i]/(double)stepm;
-           for(j2=1; j2<=nlstate;j2++){
+       /* bias is positive if real duration
-             cptj2= (j2-1)*nlstate+i2;
+        * is higher than the multiple of stepm and negative otherwise.
-             if(cptj2 <= cptj)
+        */
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-           }
+         lli=log(out[s1][s2] - savm[s1][s2]);
-       }
+       } else if  ( s2==-1 ) { /* alive */
-     fprintf(ficrescveij,"\n");
+         for (j=1,survp=0. ; j<=nlstate; j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   }
+         lli= log(survp);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+       }else if (mle==1){
-   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);
+       } else if(mle==2){
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+         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(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         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 */
-   printf("\n");
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   fprintf(ficlog,"\n");
+         lli=log(out[s1][s2]); /* Original formula */
+       } else{  /* mle=0 back to 1 */
-   free_vector(xm,1,npar);
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   free_vector(xp,1,npar);
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+       } /* End of if */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+       ipmx +=1;
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+       sw += weight[i];
- }
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
- /************ Variance ******************/
+       if(globpr){
- 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[])
+         fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
- {
+  %11.6f %11.6f %11.6f ", \
-   /* Variance of health expectancies */
+                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-   /* double **newm;*/
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   double **dnewm,**doldm;
+           llt +=ll[k]*gipmx/gsw;
-   double **dnewmp,**doldmp;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   int i, j, nhstepm, hstepm, h, nstepm ;
+         }
-   int k, cptcode;
+         fprintf(ficresilk," %10.6f\n", -llt);
-   double *xp;
+       }
-   double **gp, **gm;  /* for var eij */
+     } /* end of wave */
-   double ***gradg, ***trgradg; /*for var eij */
+   } /* end of individual */
-   double **gradgp, **trgradgp; /* for var p point j */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   double *gpp, *gmp; /* for var p point j */
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   double ***p3mat;
+   if(globpr==0){ /* First time we count the contributions and weights */
-   double age,agelim, hf;
+     gipmx=ipmx;
-   double ***mobaverage;
+     gsw=sw;
-   int theta;
+   }
-   char digit[4];
+   return -l;
-   char digitp[25];
+ }
-   char fileresprobmorprev[FILENAMELENGTH];
+ /*************** function likelione ***********/
-   if(popbased==1){
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     if(mobilav!=0)
+ {
-       strcpy(digitp,"-populbased-mobilav-");
+   /* This routine should help understanding what is done with
-     else strcpy(digitp,"-populbased-nomobil-");
+      the selection of individuals/waves and
-   }
+      to check the exact contribution to the likelihood.
-   else
+      Plotting could be done.
-     strcpy(digitp,"-stablbased-");
+    */
+   int k;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     strcpy(fileresilk,"ILK_");
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     strcat(fileresilk,fileresu);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-     }
+       printf("Problem with resultfile: %s\n", fileresilk);
-   }
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
-   strcpy(fileresprobmorprev,"prmorprev");
+     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");
-   sprintf(digit,"%-d",ij);
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+     for(k=1; k<=nlstate; k++)
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   strcat(fileresprobmorprev,fileres);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   }
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   *fretone=(*funcone)(p);
-   }
+   if(*globpri !=0){
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     fclose(ficresilk);
+     if (mle ==0)
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-   pstamp(ficresprobmorprev);
+     else if(mle >=1)
-   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(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+     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));
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
+     for (k=1; k<= nlstate ; k++) {
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
-   }
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
-   fprintf(ficresprobmorprev,"\n");
+     }
-   fprintf(ficgp,"\n# Routine varevsij");
+     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> \
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
- /*   } */
+     fflush(fichtm);
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   }
-   pstamp(ficresvij);
+   return;
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+ }
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
-   else
+ /*********** Maximum Likelihood Estimation ***************/
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresvij,"# Age");
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   for(i=1; i<=nlstate;i++)
+ {
-     for(j=1; j<=nlstate;j++)
+   int i,j, iter=0;
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   double **xi;
-   fprintf(ficresvij,"\n");
+   double fret;
+   double fretone; /* Only one call to likelihood */
-   xp=vector(1,npar);
+   /*  char filerespow[FILENAMELENGTH];*/
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
+ #ifdef NLOPT
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   int creturn;
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   nlopt_opt opt;
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   double *lb;
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   double minf; /* the minimum objective value, upon return */
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   myfunc_data dinst, *d = &dinst;
+ #endif
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+   xi=matrix(1,npar,1,npar);
-   else  hstepm=estepm;
+   for (i=1;i<=npar;i++)
-   /* For example we decided to compute the life expectancy with the smallest unit */
+     for (j=1;j<=npar;j++)
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-      nhstepm is the number of hstepm from age to agelim
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-      nstepm is the number of stepm from age to agelin.
+   strcpy(filerespow,"POW_");
-      Look at hpijx to understand the reason of that which relies in memory size
+   strcat(filerespow,fileres);
-      and note for a fixed period like k years */
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     printf("Problem with resultfile: %s\n", filerespow);
-      survival function given by stepm (the optimization length). Unfortunately it
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-      means that if the survival funtion is printed every two years of age and if
+   }
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-      results. So we changed our mind and took the option of the best precision.
+   for (i=1;i<=nlstate;i++)
-   */
+     for(j=1;j<=nlstate+ndeath;j++)
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   agelim = AGESUP;
+   fprintf(ficrespow,"\n");
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ #ifdef POWELL
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ #endif
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+ #ifdef NLOPT
-     gp=matrix(0,nhstepm,1,nlstate);
+ #ifdef NEWUOA
-     gm=matrix(0,nhstepm,1,nlstate);
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-     for(theta=1; theta <=npar; theta++){
+ #endif
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   lb=vector(0,npar-1);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-       }
+   nlopt_set_lower_bounds(opt, lb);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   nlopt_set_initial_step1(opt, 0.1);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-       if (popbased==1) {
+   d->function = func;
-         if(mobilav ==0){
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-           for(i=1; i<=nlstate;i++)
+   nlopt_set_min_objective(opt, myfunc, d);
-             prlim[i][i]=probs[(int)age][i][ij];
+   nlopt_set_xtol_rel(opt, ftol);
-         }else{ /* mobilav */
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-           for(i=1; i<=nlstate;i++)
+     printf("nlopt failed! %d\n",creturn);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   }
-         }
+   else {
-       }
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-       for(j=1; j<= nlstate; j++){
+     iter=1; /* not equal */
-         for(h=0; h<=nhstepm; h++){
+   }
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+   nlopt_destroy(opt);
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+ #endif
-         }
+   free_matrix(xi,1,npar,1,npar);
-       }
+   fclose(ficrespow);
-       /* This for computing probability of death (h=1 means
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-          computed over hstepm matrices product = hstepm*stepm months)
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-          as a weighted average of prlim.
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+ }
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+ /**** Computes Hessian and covariance matrix ***/
-       }
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-       /* end probability of death */
+ {
+   double  **a,**y,*x,pd;
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+   /* double **hess; */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   int i, j;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   int *indx;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-       if (popbased==1) {
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
-         if(mobilav ==0){
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-           for(i=1; i<=nlstate;i++)
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-             prlim[i][i]=probs[(int)age][i][ij];
+   double gompertz(double p[]);
-         }else{ /* mobilav */
+   /* hess=matrix(1,npar,1,npar); */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-         }
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-       }
+   for (i=1;i<=npar;i++){
+     printf("%d-",i);fflush(stdout);
-       for(j=1; j<= nlstate; j++){
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
+     /*  printf(" %f ",p[i]);
-       }
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-       /* This for computing probability of death (h=1 means
+   }
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+   for (i=1;i<=npar;i++) {
-       */
+     for (j=1;j<=npar;j++)  {
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       if (j>i) {
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+         printf(".%d-%d",i,j);fflush(stdout);
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-       }
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
-       /* end probability of death */
+         hess[j][i]=hess[i][j];
-       for(j=1; j<= nlstate; j++) /* vareij */
+         /*printf(" %lf ",hess[i][j]);*/
-         for(h=0; h<=nhstepm; h++){
+       }
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+     }
-         }
+   }
+   printf("\n");
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   fprintf(ficlog,"\n");
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-       }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-     } /* End theta */
+   a=matrix(1,npar,1,npar);
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   y=matrix(1,npar,1,npar);
+   x=vector(1,npar);
-     for(h=0; h<=nhstepm; h++) /* veij */
+   indx=ivector(1,npar);
-       for(j=1; j<=nlstate;j++)
+   for (i=1;i<=npar;i++)
-         for(theta=1; theta <=npar; theta++)
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   ludcmp(a,npar,indx,&pd);
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   for (j=1;j<=npar;j++) {
-       for(theta=1; theta <=npar; theta++)
+     for (i=1;i<=npar;i++) x[i]=0;
-         trgradgp[j][theta]=gradgp[theta][j];
+     x[j]=1;
+     lubksb(a,npar,indx,x);
+     for (i=1;i<=npar;i++){
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       matcov[i][j]=x[i];
-     for(i=1;i<=nlstate;i++)
+     }
-       for(j=1;j<=nlstate;j++)
+   }
-         vareij[i][j][(int)age] =0.;
+   printf("\n#Hessian matrix#\n");
-     for(h=0;h<=nhstepm;h++){
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-       for(k=0;k<=nhstepm;k++){
+   for (i=1;i<=npar;i++) {
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+     for (j=1;j<=npar;j++) {
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+       printf("%.6e ",hess[i][j]);
-         for(i=1;i<=nlstate;i++)
+       fprintf(ficlog,"%.6e ",hess[i][j]);
-           for(j=1;j<=nlstate;j++)
+     }
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+     printf("\n");
-       }
+     fprintf(ficlog,"\n");
-     }
+   }
-     /* pptj */
+   /* printf("\n#Covariance matrix#\n"); */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+   /* for (i=1;i<=npar;i++) {  */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+   /*   for (j=1;j<=npar;j++) {  */
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+   /*     printf("%.6e ",matcov[i][j]); */
-         varppt[j][i]=doldmp[j][i];
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
-     /* end ppptj */
+   /*   } */
-     /*  x centered again */
+   /*   printf("\n"); */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   /*   fprintf(ficlog,"\n"); */
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   /* } */
-     if (popbased==1) {
+   /* Recompute Inverse */
-       if(mobilav ==0){
+   /* for (i=1;i<=npar;i++) */
-         for(i=1; i<=nlstate;i++)
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-           prlim[i][i]=probs[(int)age][i][ij];
+   /* ludcmp(a,npar,indx,&pd); */
-       }else{ /* mobilav */
-         for(i=1; i<=nlstate;i++)
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
-           prlim[i][i]=mobaverage[(int)age][i][ij];
-       }
+   /* for (j=1;j<=npar;j++) { */
-     }
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
-     /* This for computing probability of death (h=1 means
+   /*   lubksb(a,npar,indx,x); */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+   /*   for (i=1;i<=npar;i++){  */
-        as a weighted average of prlim.
+   /*     y[i][j]=x[i]; */
-     */
+   /*     printf("%.3e ",y[i][j]); */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   /*   } */
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   /*   printf("\n"); */
-     }
+   /*   fprintf(ficlog,"\n"); */
-     /* end probability of death */
+   /* } */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+   /* Verifying the inverse matrix */
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+ #ifdef DEBUGHESS
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
-       }
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
-     }
-     fprintf(ficresprobmorprev,"\n");
+   for (j=1;j<=npar;j++) {
+     for (i=1;i<=npar;i++){
-     fprintf(ficresvij,"%.0f ",age );
+       printf("%.2f ",y[i][j]);
-     for(i=1; i<=nlstate;i++)
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       for(j=1; j<=nlstate;j++){
+     }
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+     printf("\n");
-       }
+     fprintf(ficlog,"\n");
-     fprintf(ficresvij,"\n");
+   }
-     free_matrix(gp,0,nhstepm,1,nlstate);
+ #endif
-     free_matrix(gm,0,nhstepm,1,nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+   free_matrix(a,1,npar,1,npar);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   free_matrix(y,1,npar,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_vector(x,1,npar);
-   } /* End age */
+   free_ivector(indx,1,npar);
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+   /* free_matrix(hess,1,npar,1,npar); */
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+ }
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+ /*************** hessian matrix ****************/
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   int i;
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   int l=1, lmax=20;
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+   double k1,k2, res, fx;
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   double p2[MAXPARM+1]; /* identical to x */
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   int k=0,kmax=10;
-   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);
+   double l1;
-   /*  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);
- */
+   fx=func(x);
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
+     l1=pow(10,l);
-   free_vector(xp,1,npar);
+     delts=delt;
-   free_matrix(doldm,1,nlstate,1,nlstate);
+     for(k=1 ; k <kmax; k=k+1){
-   free_matrix(dnewm,1,nlstate,1,npar);
+       delt = delta*(l1*k);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       p2[theta]=x[theta] +delt;
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       p2[theta]=x[theta]-delt;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       k2=func(p2)-fx;
-   fclose(ficresprobmorprev);
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   fflush(ficgp);
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
-   fflush(fichtm);
- }  /* end varevsij */
+ #ifdef DEBUGHESSII
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
- /************ Variance of prevlim ******************/
+       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);
- 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[])
+ #endif
- {
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   /* Variance of prevalence limit */
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+         k=kmax;
-   double **newm;
+       }
-   double **dnewm,**doldm;
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   int i, j, nhstepm, hstepm;
+         k=kmax; l=lmax*10;
-   int k, cptcode;
+       }
-   double *xp;
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   double *gp, *gm;
+         delts=delt;
-   double **gradg, **trgradg;
+       }
-   double age,agelim;
+     } /* End loop k */
-   int theta;
+   }
+   delti[theta]=delts;
-   pstamp(ficresvpl);
+   return res;
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+ }
-   for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %1d-%1d",i,i);
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-   fprintf(ficresvpl,"\n");
+ {
+   int i;
-   xp=vector(1,npar);
+   int l=1, lmax=20;
-   dnewm=matrix(1,nlstate,1,npar);
+   double k1,k2,k3,k4,res,fx;
-   doldm=matrix(1,nlstate,1,nlstate);
+   double p2[MAXPARM+1];
+   int k, kmax=1;
-   hstepm=1*YEARM; /* Every year of age */
+   double v1, v2, cv12, lc1, lc2;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+   int firstime=0;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   fx=func(x);
-     if (stepm >= YEARM) hstepm=1;
+   for (k=1; k<=kmax; k=k+10) {
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-     gradg=matrix(1,npar,1,nlstate);
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     gp=vector(1,nlstate);
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-     gm=vector(1,nlstate);
+     k1=func(p2)-fx;
-     for(theta=1; theta <=npar; theta++){
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     k2=func(p2)-fx;
-       }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-       for(i=1;i<=nlstate;i++)
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-         gp[i] = prlim[i][i];
+     k3=func(p2)-fx;
-       for(i=1; i<=npar; i++) /* Computes gradient */
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     k4=func(p2)-fx;
-       for(i=1;i<=nlstate;i++)
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
-         gm[i] = prlim[i][i];
+     if(k1*k2*k3*k4 <0.){
+       firstime=1;
-       for(i=1;i<=nlstate;i++)
+       kmax=kmax+10;
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+     }
-     } /* End theta */
+     if(kmax >=10 || firstime ==1){
+       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);
-     trgradg =matrix(1,nlstate,1,npar);
+       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);
+       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(j=1; j<=nlstate;j++)
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-       for(theta=1; theta <=npar; theta++)
+     }
-         trgradg[j][theta]=gradg[theta][j];
+ #ifdef DEBUGHESSIJ
+     v1=hess[thetai][thetai];
-     for(i=1;i<=nlstate;i++)
+     v2=hess[thetaj][thetaj];
-       varpl[i][(int)age] =0.;
+     cv12=res;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     /* Computing eigen value of Hessian matrix */
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     for(i=1;i<=nlstate;i++)
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     if ((lc2 <0) || (lc1 <0) ){
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-     fprintf(ficresvpl,"%.0f ",age );
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-     for(i=1; i<=nlstate;i++)
+       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(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-     fprintf(ficresvpl,"\n");
+     }
-     free_vector(gp,1,nlstate);
+ #endif
-     free_vector(gm,1,nlstate);
+   }
-     free_matrix(gradg,1,npar,1,nlstate);
+   return res;
-     free_matrix(trgradg,1,nlstate,1,npar);
+ }
-   } /* End age */
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
-   free_vector(xp,1,npar);
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
-   free_matrix(doldm,1,nlstate,1,npar);
+ /* { */
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+ /*   int i; */
+ /*   int l=1, lmax=20; */
- }
+ /*   double k1,k2,k3,k4,res,fx; */
+ /*   double p2[MAXPARM+1]; */
- /************ Variance of one-step probabilities  ******************/
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+ /*   int k=0,kmax=10; */
- {
+ /*   double l1; */
-   int i, j=0,  i1, k1, l1, t, tj;
-   int k2, l2, j1,  z1;
+ /*   fx=func(x); */
-   int k=0,l, cptcode;
+ /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
-   int first=1, first1;
+ /*     l1=pow(10,l); */
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+ /*     delts=delt; */
-   double **dnewm,**doldm;
+ /*     for(k=1 ; k <kmax; k=k+1){ */
-   double *xp;
+ /*       delt = delti*(l1*k); */
-   double *gp, *gm;
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
-   double **gradg, **trgradg;
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-   double **mu;
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-   double age,agelim, cov[NCOVMAX];
+ /*       k1=func(p2)-fx; */
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-   char fileresprob[FILENAMELENGTH];
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-   char fileresprobcov[FILENAMELENGTH];
+ /*       k2=func(p2)-fx; */
-   char fileresprobcor[FILENAMELENGTH];
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-   double ***varpij;
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k3=func(p2)-fx; */
-   strcpy(fileresprob,"prob");
-   strcat(fileresprob,fileres);
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-     printf("Problem with resultfile: %s\n", fileresprob);
+ /*       k4=func(p2)-fx; */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
-   }
+ /* #ifdef DEBUGHESSIJ */
-   strcpy(fileresprobcov,"probcov");
+ /*       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); */
-   strcat(fileresprobcov,fileres);
+ /*       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); */
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+ /* #endif */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+ /*      k=kmax; */
-   }
+ /*       } */
-   strcpy(fileresprobcor,"probcor");
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
-   strcat(fileresprobcor,fileres);
+ /*      k=kmax; l=lmax*10; */
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+ /*       } */
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+ /*      delts=delt; */
-   }
+ /*       } */
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ /*     } /\* End loop k *\/ */
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ /*   } */
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ /*   delti[theta]=delts; */
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ /*   return res;  */
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+ /* } */
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+ /************** Inverse of matrix **************/
-   fprintf(ficresprob,"# Age");
+ void ludcmp(double **a, int n, int *indx, double *d)
-   pstamp(ficresprobcov);
+ {
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   int i,imax,j,k;
-   fprintf(ficresprobcov,"# Age");
+   double big,dum,sum,temp;
-   pstamp(ficresprobcor);
+   double *vv;
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"# Age");
+   vv=vector(1,n);
+   *d=1.0;
+   for (i=1;i<=n;i++) {
-   for(i=1; i<=nlstate;i++)
+     big=0.0;
-     for(j=1; j<=(nlstate+ndeath);j++){
+     for (j=1;j<=n;j++)
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     vv[i]=1.0/big;
-     }
+   }
-  /* fprintf(ficresprob,"\n");
+   for (j=1;j<=n;j++) {
-   fprintf(ficresprobcov,"\n");
+     for (i=1;i<j;i++) {
-   fprintf(ficresprobcor,"\n");
+       sum=a[i][j];
-  */
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-  xp=vector(1,npar);
+       a[i][j]=sum;
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+     }
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+     big=0.0;
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     for (i=j;i<=n;i++) {
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+       sum=a[i][j];
-   first=1;
+       for (k=1;k<j;k++)
-   fprintf(ficgp,"\n# Routine varprob");
+         sum -= a[i][k]*a[k][j];
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+       a[i][j]=sum;
-   fprintf(fichtm,"\n");
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
+         big=dum;
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+         imax=i;
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+       }
-   file %s<br>\n",optionfilehtmcov);
+     }
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+     if (j != imax) {
- and drawn. It helps understanding how is the covariance between two incidences.\
+       for (k=1;k<=n;k++) {
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+         dum=a[imax][k];
-   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. \
+         a[imax][k]=a[j][k];
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+         a[j][k]=dum;
- 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>\
+       *d = -(*d);
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+       vv[imax]=vv[j];
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+     }
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     indx[j]=imax;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   cov[1]=1;
+     if (j != n) {
-   tj=cptcoveff;
+       dum=1.0/(a[j][j]);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   j1=0;
+     }
-   for(t=1; t<=tj;t++){
+   }
-     for(i1=1; i1<=ncodemax[t];i1++){
+   free_vector(vv,1,n);  /* Doesn't work */
-       j1++;
+ ;
-       if  (cptcovn>0) {
+ }
-         fprintf(ficresprob, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ void lubksb(double **a, int n, int *indx, double b[])
-         fprintf(ficresprob, "**********\n#\n");
+ {
-         fprintf(ficresprobcov, "\n#********** Variable ");
+   int i,ii=0,ip,j;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   double sum;
-         fprintf(ficresprobcov, "**********\n#\n");
+   for (i=1;i<=n;i++) {
-         fprintf(ficgp, "\n#********** Variable ");
+     ip=indx[i];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     sum=b[ip];
-         fprintf(ficgp, "**********\n#\n");
+     b[ip]=b[i];
+     if (ii)
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+     else if (sum) ii=i;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     b[i]=sum;
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   }
+   for (i=n;i>=1;i--) {
-         fprintf(ficresprobcor, "\n#********** Variable ");
+     sum=b[i];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-         fprintf(ficresprobcor, "**********\n#");
+     b[i]=sum/a[i][i];
-       }
+   }
+ }
-       for (age=bage; age<=fage; age ++){
-         cov[2]=age;
+ void pstamp(FILE *fichier)
-         for (k=1; k<=cptcovn;k++) {
+ {
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
-         }
+ }
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (k=1; k<=cptcovprod;k++)
+ /************ Frequencies ********************/
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+                                                                          int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],  \
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+                                                                          int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+  {  /* Some frequencies */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+          int i, m, jk, j1, bool, z1,j;
+          int iind=0, iage=0;
-         for(theta=1; theta <=npar; theta++){
+          int mi; /* Effective wave */
-           for(i=1; i<=npar; i++)
+          int first;
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+          double ***freq; /* Frequencies */
+          double *pp, **prop, *posprop, *pospropt;
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+          double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-           k=0;
+          double agebegin, ageend;
-           for(i=1; i<= (nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+          pp=vector(1,nlstate);
-               k=k+1;
+          prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-               gp[k]=pmmij[i][j];
+          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 */
-           }
+          /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
+          strcpy(fileresp,"P_");
-           for(i=1; i<=npar; i++)
+          strcat(fileresp,fileresu);
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+          /*strcat(fileresphtm,fileresu);*/
+          if((ficresp=fopen(fileresp,"w"))==NULL) {
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+                  printf("Problem with prevalence resultfile: %s\n", fileresp);
-           k=0;
+                  fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-           for(i=1; i<=(nlstate); i++){
+                  exit(0);
-             for(j=1; j<=(nlstate+ndeath);j++){
+          }
-               k=k+1;
-               gm[k]=pmmij[i][j];
+          strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
-             }
+          if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
-           }
+                  printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+                  fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+                  fflush(ficlog);
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+                  exit(70);
-         }
+          }
+          else{
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+                  fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-           for(theta=1; theta <=npar; theta++)
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-             trgradg[j][theta]=gradg[theta][j];
+ 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);
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+          }
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+          fprintf(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);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+          strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+          if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+                  printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+                  fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+                  fflush(ficlog);
+                  exit(70);
-         k=0;
+          }
-         for(i=1; i<=(nlstate); i++){
+          else{
-           for(j=1; j<=(nlstate+ndeath);j++){
+                  fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-             k=k+1;
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-             mu[k][(int) age]=pmmij[i][j];
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
-           }
+                                                  fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-         }
+          }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+          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);
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-             varpij[i][j][(int)age] = doldm[i][j];
+          freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+          j1=0;
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+          j=cptcoveff;
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
+          first=1;
-         fprintf(ficresprob,"\n%d ",(int)age);
+          /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+                         reference=low_education V1=0,V2=0
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+                         med_educ                V1=1 V2=0,
+                         high_educ               V1=0 V2=1
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+                         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+          */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+          for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+                  posproptt=0.;
-         }
+                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         i=0;
+                          scanf("%d", i);*/
-         for (k=1; k<=(nlstate);k++){
+                  for (i=-5; i<=nlstate+ndeath; i++)
-           for (l=1; l<=(nlstate+ndeath);l++){
+                          for (jk=-5; jk<=nlstate+ndeath; jk++)
-             i=i++;
+                                  for(m=iagemin; m <= iagemax+3; m++)
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+                                          freq[i][jk][m]=0;
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-             for (j=1; j<=i;j++){
+                  for (i=1; i<=nlstate; i++)  {
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+                          for(m=iagemin; m <= iagemax+3; m++)
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+                                  prop[i][m]=0;
-             }
+                          posprop[i]=0;
-           }
+                          pospropt[i]=0;
-         }/* end of loop for state */
+                  }
-       } /* end of loop for age */
+                  dateintsum=0;
-       /* Confidence intervalle of pij  */
+                  k2cpt=0;
-       /*
-         fprintf(ficgp,"\nset noparametric;unset label");
+                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+                          bool=1;
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                          if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-         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 (z1=1; z1<=cptcoveff; z1++) {
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+                                                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+                                                  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),
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-       first1=1;
+                                                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-       for (k2=1; k2<=(nlstate);k2++){
+                                          }
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+                                  } /* end z1 */
-           if(l2==k2) continue;
+                          } /* cptcovn > 0 */
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
+                          if (bool==1){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+                                  /* for(m=firstpass; m<=lastpass; m++){ */
-               if(l1==k1) continue;
+                                  for(mi=1; mi<wav[iind];mi++){
-               i=(k1-1)*(nlstate+ndeath)+l1;
+                                          m=mw[mi][iind];
-               if(i<=j) continue;
+                                          /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
-               for (age=bage; age<=fage; age ++){
+                                                         and mw[mi+1][iind]. dh depends on stepm. */
-                 if ((int)age %5==0){
+                                          agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                                          ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                                          if(m >=firstpass && m <=lastpass){
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                                                  k2=anint[m][iind]+(mint[m][iind]/12.);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+                                                  if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-                   c12=cv12/sqrt(v1*v2);
+                                                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
-                   /* Computing eigen value of matrix of covariance */
+                                                  if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                                                          prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                                                  if (m<lastpass) {
-                   /* Eigen vectors */
+                                                          /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                                                          /*   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]); */
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+                                                          if(s[m][iind]==-1)
-                   v21=(lc1-v1)/cv12*v11;
+                                                                  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.));
-                   v12=-v21;
+                                                          freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-                   v22=v11;
+                                                          /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-                   tnalp=v21/v11;
+                                                          freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
-                   if(first1==1){
+                                                  }
-                     first1=0;
+                                          }
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                                          if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
-                   }
+                                                  dateintsum=dateintsum+k2;
-                   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);
+                                                  k2cpt++;
-                   /*printf(fignu*/
+                                                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                                          }
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                                          /*}*/
-                   if(first==1){
+                                  } /* end m */
-                     first=0;
+                          } /* end bool */
-                     fprintf(ficgp,"\nset parametric;unset label");
+                  } /* end iind = 1 to imx */
-                     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);
+        /* prop[s][age] is feeded for any initial and valid live state as well as
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                                         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+                  /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                  pstamp(ficresp);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                  if  (cptcovn>0) {
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                          fprintf(ficresp, "\n#********** Variable ");
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                          for (z1=1; z1<=cptcoveff; z1++){
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                                  fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                     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(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                                  fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                          }
-                   }else{
+                          fprintf(ficresp, "**********\n#");
-                     first=0;
+                          fprintf(ficresphtm, "**********</h3>\n");
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                          fprintf(ficresphtmfr, "**********</h3>\n");
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                          fprintf(ficlog, "\n#********** Variable ");
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                     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(ficlog, "**********\n");
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                  }
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                  fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-                   }/* if first */
+                  for(i=1; i<=nlstate;i++) {
-                 } /* age mod 5 */
+                          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-               } /* end loop age */
+                          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                  }
-               first=1;
+                  fprintf(ficresp, "\n");
-             } /*l12 */
+                  fprintf(ficresphtm, "\n");
-           } /* k12 */
-         } /*l1 */
+                  /* Header of frequency table by age */
-       }/* k1 */
+                  fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-     } /* loop covariates */
+                  fprintf(ficresphtmfr,"<th>Age</th> ");
-   }
+                  for(jk=-1; jk <=nlstate+ndeath; jk++){
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+                          for(m=-1; m <=nlstate+ndeath; m++){
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+                                  if(jk!=0 && m!=0)
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+                                          fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+                          }
-   free_vector(xp,1,npar);
+                  }
-   fclose(ficresprob);
+                  fprintf(ficresphtmfr, "\n");
-   fclose(ficresprobcov);
-   fclose(ficresprobcor);
+                  /* For each age */
-   fflush(ficgp);
+                  for(iage=iagemin; iage <= iagemax+3; iage++){
-   fflush(fichtmcov);
+                          fprintf(ficresphtm,"<tr>");
- }
+                          if(iage==iagemax+1){
+                                  fprintf(ficlog,"1");
+                                  fprintf(ficresphtmfr,"<tr><th>0</th> ");
- /******************* Printing html file ***********/
+                          }else if(iage==iagemax+2){
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                                  fprintf(ficlog,"0");
-                   int lastpass, int stepm, int weightopt, char model[],\
+                                  fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                          }else if(iage==iagemax+3){
-                   int popforecast, int estepm ,\
+                                  fprintf(ficlog,"Total");
-                   double jprev1, double mprev1,double anprev1, \
+                                  fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-                   double jprev2, double mprev2,double anprev2){
+                          }else{
-   int jj1, k1, i1, cpt;
+                                  if(first==1){
+                                          first=0;
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+                                          printf("See log file for details...\n");
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+                                  }
- </ul>");
+                                  fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+                                  fprintf(ficlog,"Age %d", iage);
-  - 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"));
+                          for(jk=1; jk <=nlstate ; jk++){
-    fprintf(fichtm,"\
+                                  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+                                          pp[jk] += freq[jk][m][iage];
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+                          }
-    fprintf(fichtm,"\
+                          for(jk=1; jk <=nlstate ; jk++){
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+                                  for(m=-1, pos=0; m <=0 ; m++)
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+                                          pos += freq[jk][m][iage];
-    fprintf(fichtm,"\
+                                  if(pp[jk]>=1.e-10){
-  - (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): \
+                                          if(first==1){
-    <a href=\"%s\">%s</a> <br>\n",
+                                                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+                                          }
-    fprintf(fichtm,"\
+                                          fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-  - Population projections by age and states: \
+                                  }else{
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+                                          if(first==1)
+                                                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+                                          fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                                  }
-  m=cptcoveff;
+                          }
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+                          for(jk=1; jk <=nlstate ; jk++){
-  jj1=0;
+                                  /* posprop[jk]=0; */
-  for(k1=1; k1<=m;k1++){
+                                  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+                                          pp[jk] += freq[jk][m][iage];
-      jj1++;
+                          }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-      if (cptcovn > 0) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+                          for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+                                  pos += pp[jk]; /* pos is the total number of transitions until this age */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+                                  posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-      }
+                                  pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
-      /* Pij */
+                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-      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);
+                          for(jk=1; jk <=nlstate ; jk++){
-      /* Quasi-incidences */
+                                  if(pos>=1.e-5){
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+                                          if(first==1)
-  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> \
+                                                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+                                          fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-        /* Period (stable) prevalence in each health state */
+                                  }else{
-        for(cpt=1; cpt<nlstate;cpt++){
+                                          if(first==1)
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+                                                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+                                          fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-        }
+                                  }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+                                  if( iage <= iagemax){
-         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> \
+                                          if(pos>=1.e-5){
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+                                                  fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-      }
+                                                  fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-    } /* end i1 */
+                                                  /*probs[iage][jk][j1]= pp[jk]/pos;*/
-  }/* End k1 */
+                                                  /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
-  fprintf(fichtm,"</ul>");
+                                          }
+                                          else{
+                                                  fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
-  fprintf(fichtm,"\
+                                                  fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+                                          }
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+                                  }
+                                  pospropt[jk] +=posprop[jk];
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                          } /* end loop jk */
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+                          /* pospropt=0.; */
-  fprintf(fichtm,"\
+                          for(jk=-1; jk <=nlstate+ndeath; jk++){
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                                  for(m=-1; m <=nlstate+ndeath; m++){
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+                                          if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                                                  if(first==1){
-  fprintf(fichtm,"\
+                                                          printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                                                  }
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+                                                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
-  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): \
+                                          if(jk!=0 && m!=0)
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                                                  fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+                                  }
-  fprintf(fichtm,"\
+                          } /* end loop jk */
-  - (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): \
+                          posproptt=0.;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                          for(jk=1; jk <=nlstate; jk++){
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+                                  posproptt += pospropt[jk];
-  fprintf(fichtm,"\
+                          }
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+                          fprintf(ficresphtmfr,"</tr>\n ");
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+                          if(iage <= iagemax){
-  fprintf(fichtm,"\
+                                  fprintf(ficresp,"\n");
-  - 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",
+                                  fprintf(ficresphtm,"</tr>\n");
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+                          }
-  fprintf(fichtm,"\
+                          if(first==1)
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+                                  printf("Others in log...\n");
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+                          fprintf(ficlog,"\n");
+                  } /* end loop age iage */
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+                  fprintf(ficresphtm,"<tr><th>Tot</th>");
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+                  for(jk=1; jk <=nlstate ; jk++){
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+                          if(posproptt < 1.e-5){
- /*      <br>",fileres,fileres,fileres,fileres); */
+                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
- /*  else  */
+                          }else{
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
-  fflush(fichtm);
+                          }
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+                  }
+                  fprintf(ficresphtm,"</tr>\n");
-  m=cptcoveff;
+                  fprintf(ficresphtm,"</table>\n");
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+                  fprintf(ficresphtmfr,"</table>\n");
+                  if(posproptt < 1.e-5){
-  jj1=0;
+                          fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-  for(k1=1; k1<=m;k1++){
+                          fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+                          fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
-      jj1++;
+                          invalidvarcomb[j1]=1;
-      if (cptcovn > 0) {
+                  }else{
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+                          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+                          invalidvarcomb[j1]=0;
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+                  }
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+                  fprintf(ficresphtmfr,"</table>\n");
-      }
+          } /* end selected combination of covariate j1 */
-      for(cpt=1; cpt<=nlstate;cpt++) {
+          dateintmean=dateintsum/k2cpt;
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+          fclose(ficresp);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+          fclose(ficresphtm);
-      }
+          fclose(ficresphtmfr);
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
- health expectancies in states (1) and (2): %s%d.png<br>\
+          free_vector(pospropt,1,nlstate);
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+          free_vector(posprop,1,nlstate);
-    } /* end i1 */
+          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
-  }/* End k1 */
+          free_vector(pp,1,nlstate);
-  fprintf(fichtm,"</ul>");
+          /* End of Freq */
-  fflush(fichtm);
+  }
- }
+ /************ Prevalence ********************/
- /******************* Gnuplot file **************/
+ 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)
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ {
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-   char dirfileres[132],optfileres[132];
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+      We still use firstpass and lastpass as another selection.
-   int ng;
+   */
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
- /*     printf("Problem with file %s",optionfilegnuplot); */
+   int i, m, jk, j1, bool, z1,j;
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   int mi; /* Effective wave */
- /*   } */
+   int iage;
+   double agebegin, ageend;
-   /*#ifdef windows */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   double **prop;
-     /*#endif */
+   double posprop;
-   m=pow(2,cptcoveff);
+   double  y2; /* in fractional years */
+   int iagemin, iagemax;
-   strcpy(dirfileres,optionfilefiname);
+   int first; /** to stop verbosity which is redirected to log file */
-   strcpy(optfileres,"vpl");
-  /* 1eme*/
+   iagemin= (int) agemin;
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   iagemax= (int) agemax;
-    for (k1=1; k1<= m ; k1 ++) {
+   /*pp=vector(1,nlstate);*/
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+   j1=0;
- set ylabel \"Probability\" \n\
- set ter png small\n\
+   /*j=cptcoveff;*/
- set size 0.65,0.65\n\
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+   first=1;
-      for (i=1; i<= nlstate ; i ++) {
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+     for (i=1; i<=nlstate; i++)
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-      }
+                                 prop[i][iage]=0.0;
-      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 (i=1; i<=imx; i++) { /* Each individual */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       bool=1;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-      }
+                                 for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+                                         if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
-      for (i=1; i<= nlstate ; i ++) {
+                                                 bool=0;
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       }
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       if (bool==1) { /* For this combination of covariates values, this individual fits */
-      }
+                                 /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+                                 for(mi=1; mi<wav[i];mi++){
-    }
+                                         m=mw[mi][i];
-   }
+                                         agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-   /*2 eme*/
+                                         /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+                                         if(m >=firstpass && m <=lastpass){
-   for (k1=1; k1<= m ; k1 ++) {
+                                                 y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+                                                 if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+                                                         if(agev[m][i]==0) agev[m][i]=iagemax+1;
+                                                         if(agev[m][i]==1) agev[m][i]=iagemax+2;
-     for (i=1; i<= nlstate+1 ; i ++) {
+                                                         if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
-       k=2*i;
+                                                                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                                 exit(1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                         }
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                                                         if (s[m][i]>0 && s[m][i]<=nlstate) {
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                                                 /*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];/* At age of beginning of transition, where status is known */
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+                                                                 prop[s[m][i]][iagemax+3] += weight[i];
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+                                                         } /* end valid statuses */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                 } /* end selection of dates */
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                         } /* end selection of waves */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                                 } /* end effective waves */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       } /* end bool */
-       }
+     }
-       fprintf(ficgp,"\" t\"\" w l 0,");
+     for(i=iagemin; i <= iagemax+3; i++){
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                 posprop += prop[jk][i];
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       }
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+       for(jk=1; jk <=nlstate ; jk++){
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+                                 if( i <=  iagemax){
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+                                         if(posprop>=1.e-5){
-     }
+                                                 probs[i][jk][j1]= prop[jk][i]/posprop;
-   }
+                                         } else{
+                                                 if(first==1){
-   /*3eme*/
+                                                         first=0;
+                                                         printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-   for (k1=1; k1<= m ; k1 ++) {
+                                                 }
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+                                         }
-       /*       k=2+nlstate*(2*cpt-2); */
+                                 }
-       k=2+(nlstate+1)*(cpt-1);
+       }/* end jk */
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+     }/* end i */
-       fprintf(ficgp,"set ter png small\n\
+     /*} *//* end i1 */
- set size 0.65,0.65\n\
+   } /* end j1 */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+   /*free_vector(pp,1,nlstate);*/
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ }  /* End of prevalence */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ /************* Waves Concatenation ***************/
-       */
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
-       for (i=1; i< nlstate ; i ++) {
+ {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-         /*      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);*/
+      Death is a valid wave (if date is known).
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-       }
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+      and mw[mi+1][i]. dh depends on stepm.
-     }
+      */
-   }
+   int i, mi, m;
-   /* CV preval stable (period) */
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   for (k1=1; k1<= m ; k1 ++) {
+      double sum=0., jmean=0.;*/
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+   int first, firstwo, firsthree, firstfour;
-       k=3;
+   int j, k=0,jk, ju, jl;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+   double sum=0.;
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+   first=0;
- set ter png small\nset size 0.65,0.65\n\
+   firstwo=0;
- unset log y\n\
+   firsthree=0;
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+   firstfour=0;
+   jmin=100000;
-       for (i=1; i< nlstate ; i ++)
+   jmax=-1;
-         fprintf(ficgp,"+$%d",k+i+1);
+   jmean=0.;
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
+     mi=0;
-       l=3+(nlstate+ndeath)*cpt;
+     m=firstpass;
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+     while(s[m][i] <= nlstate){  /* a live state */
-       for (i=1; i< nlstate ; i ++) {
+       if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
-         l=3+(nlstate+ndeath)*cpt;
+         mw[++mi][i]=m;
-         fprintf(ficgp,"+$%d",l+i+1);
+       }
-       }
+       if(m >=lastpass){
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
-     }
+           if(firsthree == 0){
-   }
+             printf("Information! Unknown health 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.\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;
-   /* proba elementaires */
+           }
-   for(i=1,jk=1; i <=nlstate; i++){
+           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.\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(k=1; k <=(nlstate+ndeath); k++){
+           mw[++mi][i]=m;
-       if (k != i) {
+         }
-         for(j=1; j <=ncovmodel; j++){
+         if(s[m][i]==-2){ /* Vital status is really unknown */
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           nbwarn++;
-           jk++;
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
-           fprintf(ficgp,"\n");
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
-         }
+             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\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);
-       }
+           }
-     }
+           break;
-    }
+         }
+         break;
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+       }
-      for(jk=1; jk <=m; jk++) {
+       else
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+         m++;
-        if (ng==2)
+     }/* end while */
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-        else
+     /* After last pass */
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+     if (s[m][i] > nlstate){  /* In a death state */
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       mi++;     /* Death is another wave */
-        i=1;
+       /* if(mi==0)  never been interviewed correctly before death */
-        for(k2=1; k2<=nlstate; k2++) {
+          /* Only death is a correct wave */
-          k3=i;
+       mw[mi][i]=m;
-          for(k=1; k<=(nlstate+ndeath); k++) {
+     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
-            if (k != k2){
+       /* m++; */
-              if(ng==2)
+       /* mi++; */
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
-              else
+       /* mw[mi][i]=m; */
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+       nberr++;
-              ij=1;
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-              for(j=3; j <=ncovmodel; j++) {
+         if(firstwo==0){
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+           printf("Error! Death for individual %ld line=%d  occurred %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 );
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+           firstwo=1;
-                  ij++;
+         }
-                }
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %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 );
-                else
+       }else{ /* end date of interview is known */
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         /* death is known but not confirmed by death status at any wave */
-              }
+         if(firstfour==0){
-              fprintf(ficgp,")/(1");
+           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 );
+           firstfour=1;
-              for(k1=1; k1 <=nlstate; k1++){
+         }
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. 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 );
-                ij=1;
+       }
-                for(j=3; j <=ncovmodel; j++){
+     }
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     wav[i]=mi;
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+     if(mi==0){
-                    ij++;
+       nbwarn++;
-                  }
+       if(first==0){
-                  else
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         first=1;
-                }
+       }
-                fprintf(ficgp,")");
+       if(first==1){
-              }
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       }
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+     } /* end mi==0 */
-              i=i+ncovmodel;
+   } /* End individuals */
-            }
+   /* wav and mw are no more changed */
-          } /* end k */
-        } /* end k2 */
-      } /* end jk */
+   for(i=1; i<=imx; i++){
-    } /* end ng */
+     for(mi=1; mi<wav[i];mi++){
-    fflush(ficgp);
+       if (stepm <=0)
- }  /* end gnuplot */
+         dh[mi][i]=1;
+       else{
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
- /*************** Moving average **************/
+           if (agedc[i] < 2*AGESUP) {
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   int i, cpt, cptcod;
+             else if(j<0){
-   int modcovmax =1;
+               nberr++;
-   int mobilavrange, mob;
+               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]);
-   double age;
+               j=1; /* Temporary Dangerous patch */
+               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);
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+               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]);
-                            a covariate has 2 modalities */
+               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);
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+             }
+             k=k+1;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+             if (j >= jmax){
-     if(mobilav==1) mobilavrange=5; /* default */
+               jmax=j;
-     else mobilavrange=mobilav;
+               ijmax=i;
-     for (age=bage; age<=fage; age++)
+             }
-       for (i=1; i<=nlstate;i++)
+             if (j <= jmin){
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+               jmin=j;
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+               ijmin=i;
-     /* 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
+             sum=sum+j;
-        we use a 5 terms etc. until the borders are no more concerned.
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-     */
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-     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++){
+         else{
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+ /*        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]); */
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+           k=k+1;
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+           if (j >= jmax) {
-               }
+             jmax=j;
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+             ijmax=i;
            }
-         }
+           else if (j <= jmin){
-       }/* end age */
+             jmin=j;
-     }/* end mob */
+             ijmin=i;
-   }else return -1;
+           }
-   return 0;
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
- }/* End movingaverage */
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+           if(j<0){
+             nberr++;
- /************** Forecasting ******************/
+             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]);
- 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){
+             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]);
-   /* proj1, year, month, day of starting projection
+           }
-      agemin, agemax range of age
+           sum=sum+j;
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+         }
-      anproj2 year of en of projection (same day and month as proj1).
+         jk= j/stepm;
-   */
+         jl= j -jk*stepm;
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+         ju= j -(jk+1)*stepm;
-   int *popage;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-   double agec; /* generic age */
+           if(jl==0){
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+             dh[mi][i]=jk;
-   double *popeffectif,*popcount;
+             bh[mi][i]=0;
-   double ***p3mat;
+           }else{ /* We want a negative bias in order to only have interpolation ie
-   double ***mobaverage;
+                   * to avoid the price of an extra matrix product in likelihood */
-   char fileresf[FILENAMELENGTH];
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
-   agelim=AGESUP;
+           }
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         }else{
+           if(jl <= -ju){
-   strcpy(fileresf,"f");
+             dh[mi][i]=jk;
-   strcat(fileresf,fileres);
+             bh[mi][i]=jl;       /* bias is positive if real duration
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+                                  * is higher than the multiple of stepm and negative otherwise.
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+                                  */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+           }
-   }
+           else{
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+             dh[mi][i]=jk+1;
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+             bh[mi][i]=ju;
+           }
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+           if(dh[mi][i]==0){
+             dh[mi][i]=1; /* At least one step */
-   if (mobilav!=0) {
+             bh[mi][i]=ju; /* At least one step */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             /*  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 (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+           }
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         } /* end if mle */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
-     }
+     } /* end wave */
    }
+   jmean=sum/k;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   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);
-   if (stepm<=12) stepsize=1;
+   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);
-   if(estepm < stepm){
+  }
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+ /*********** Tricode ****************************/
-   else  hstepm=estepm;
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
+ {
-   hstepm=hstepm/stepm;
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-                                fractional in yp1 */
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-   anprojmean=yp;
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-   yp2=modf((yp1*12),&yp);
+    * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
-   mprojmean=yp;
+   */
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   if(jprojmean==0) jprojmean=1;
+   int modmaxcovj=0; /* Modality max of covariates j */
-   if(mprojmean==0) jprojmean=1;
+   int cptcode=0; /* Modality max of covariates j */
+   int modmincovj=0; /* Modality min of covariates j */
-   i1=cptcoveff;
-   if (cptcovn < 1){i1=1;}
+   /* cptcoveff=0;  */
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+         *cptcov=0;
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
- /*            if (h==(int)(YEARM*yearp)){ */
+   /* Loop on covariates without age and products */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     for (k=-1; k < maxncov; k++) Ndum[k]=0;
-       k=k+1;
+     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
-       fprintf(ficresf,"\n#******");
+                                                                                                                                 modality of this covariate Vj*/
-       for(j=1;j<=cptcoveff;j++) {
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-         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]]);
+                                                                                                                                                 * If product of Vn*Vm, still boolean *:
-       }
+                                                                                                                                                 * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-       fprintf(ficresf,"******\n");
+                                                                                                                                                 * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       for(j=1; j<=nlstate+ndeath;j++){
+                                       modality of the nth covariate of individual i. */
-         for(i=1; i<=nlstate;i++)
+       if (ij > modmaxcovj)
-           fprintf(ficresf," p%d%d",i,j);
+         modmaxcovj=ij;
-         fprintf(ficresf," p.%d",j);
+       else if (ij < modmincovj)
-       }
+                                 modmincovj=ij;
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       if ((ij < -1) && (ij > NCOVMAX)){
-         fprintf(ficresf,"\n");
+                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+                                 exit(1);
+       }else
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-           nhstepm = nhstepm/hstepm;
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* getting the maximum value of the modality of the covariate
-           oldm=oldms;savm=savms;
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+          female is 1, then modmaxcovj=1.*/
+     } /* end for loop on individuals i */
-           for (h=0; h<=nhstepm; h++){
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-             if (h*hstepm/YEARM*stepm ==yearp) {
+     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-               fprintf(ficresf,"\n");
+     cptcode=modmaxcovj;
-               for(j=1;j<=cptcoveff;j++)
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    /*for (i=0; i<=cptcode; i++) {*/
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-             }
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-             for(j=1; j<=nlstate+ndeath;j++) {
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-               ppij=0.;
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
-               for(i=1; i<=nlstate;i++) {
+                                 if( k != -1){
-                 if (mobilav==1)
+                                         ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                                                                                                                  covariate for which somebody answered excluding
-                 else {
+                                                                                                                  undefined. Usually 2: 0 and 1. */
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                                 }
-                 }
+                                 ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
-                 if (h*hstepm/YEARM*stepm== yearp) {
+                                                                                                                                 covariate for which somebody answered including
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
-                 }
+       }
-               } /* end i */
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-               if (h*hstepm/YEARM*stepm==yearp) {
+                                  historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-                 fprintf(ficresf," %.3f", ppij);
+     } /* Ndum[-1] number of undefined modalities */
-               }
-             }/* end j */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-           } /* end h */
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
-         } /* end agec */
+        modmincovj=3; modmaxcovj = 7;
-       } /* end yearp */
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-     } /* end cptcod */
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-   } /* end  cptcov */
+        defining two dummy variables: variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        nbcode[Tvar[j]][1]=0;
+        nbcode[Tvar[j]][2]=1;
-   fclose(ficresf);
+        nbcode[Tvar[j]][3]=2;
- }
+        To be continued (not working yet).
+     */
- /************** Forecasting *****not tested NB*************/
+     ij=0; /* ij is similar to i but can jump over null modalities */
- 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){
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+                                 break;
-   int *popage;
+                         }
-   double calagedatem, agelim, kk1, kk2;
+         ij++;
-   double *popeffectif,*popcount;
+         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
-   double ***p3mat,***tabpop,***tabpopprev;
+         cptcode = ij; /* New max modality for covar j */
-   double ***mobaverage;
+     } /* end of loop on modality i=-1 to 1 or more */
-   char filerespop[FILENAMELENGTH];
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /*  /\*recode from 0 *\/ */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /*                               k is a modality. If we have model=V1+V1*sex  */
-   agelim=AGESUP;
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+     /*  } */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+     /*  if (ij > ncodemax[j]) { */
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-   strcpy(filerespop,"pop");
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-   strcat(filerespop,fileres);
+     /*    break; */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     /*  } */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+     /*   }  /\* end of loop on modality k *\/ */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+         for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+                 /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+                 ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-   if (mobilav!=0) {
+                 Ndum[ij]++; /* Might be supersed V1 + V1*age */
-     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);
+         ij=0;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     }
+                 /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   }
+                 if((Ndum[i]!=0) && (i<=ncovcol)){
+                         ij++;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+                         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   if (stepm<=12) stepsize=1;
+                         Tvaraff[ij]=i; /*For printing (unclear) */
+                 }else{
-   agelim=AGESUP;
+                         /* Tvaraff[ij]=0; */
+                 }
-   hstepm=1;
+         }
-   hstepm=hstepm/stepm;
+         /* ij--; */
+         /* cptcoveff=ij; /\*Number of total covariates*\/ */
-   if (popforecast==1) {
+         *cptcov=ij; /*Number of total covariates*/
-     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);
+ /*********** Health Expectancies ****************/
-     popeffectif=vector(0,AGESUP);
-     popcount=vector(0,AGESUP);
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-     i=1;
+ {
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm;
-     imx=i;
+   int nhstepma, nstepma; /* Decreasing with age */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   double age, agelim, hf;
-   }
+   double ***p3mat;
+   double eip;
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   pstamp(ficreseij);
-       k=k+1;
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-       fprintf(ficrespop,"\n#******");
+   fprintf(ficreseij,"# Age");
-       for(j=1;j<=cptcoveff;j++) {
+   for(i=1; i<=nlstate;i++){
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(j=1; j<=nlstate;j++){
-       }
+       fprintf(ficreseij," e%1d%1d ",i,j);
-       fprintf(ficrespop,"******\n");
+     }
-       fprintf(ficrespop,"# Age");
+     fprintf(ficreseij," e%1d. ",i);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+   }
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+   fprintf(ficreseij,"\n");
-       for (cpt=0; cpt<=0;cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+   }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   else  hstepm=estepm;
-           nhstepm = nhstepm/hstepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-           oldm=oldms;savm=savms;
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-           for (h=0; h<=nhstepm; h++){
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+    * to compare the new estimate of Life expectancy with the same linear
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+    * hypothesis. A more precise result, taking into account a more precise
-             }
+    * curvature will be obtained if estepm is as small as stepm. */
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-               for(i=1; i<=nlstate;i++) {
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-                 if (mobilav==1)
+      nhstepm is the number of hstepm from age to agelim
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+      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
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+      and note for a fixed period like estepm months */
-                 }
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-               }
+      survival function given by stepm (the optimization length). Unfortunately it
-               if (h==(int)(calagedatem+12*cpt)){
+      means that if the survival funtion is printed only each two years of age and if
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-                   /*fprintf(ficrespop," %.3f", kk1);
+      results. So we changed our mind and took the option of the best precision.
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+   */
-               }
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-             }
-             for(i=1; i<=nlstate;i++){
+   agelim=AGESUP;
-               kk1=0.;
+   /* If stepm=6 months */
-                 for(j=1; j<=nlstate;j++){
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-                 }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+ /* nhstepm age range expressed in number of stepm */
-             }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+   /* if (stepm >= YEARM) hstepm=1;*/
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           }
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+   for (age=bage; age<=fage; age ++){
-       }
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   /******/
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+     /* If stepm=6 months */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-           nhstepm = nhstepm/hstepm;
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           for (h=0; h<=nhstepm; h++){
+     printf("%d|",(int)age);fflush(stdout);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
+     /* Computing expectancies */
-             for(j=1; j<=nlstate+ndeath;j++) {
+     for(i=1; i<=nlstate;i++)
-               kk1=0.;kk2=0;
+       for(j=1; j<=nlstate;j++)
-               for(i=1; i<=nlstate;i++) {
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-               }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+           /* 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]);*/
-             }
-           }
+         }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+     fprintf(ficreseij,"%3.0f",age );
-       }
+     for(i=1; i<=nlstate;i++){
-    }
+       eip=0;
-   }
+       for(j=1; j<=nlstate;j++){
+         eip +=eij[i][j][(int)age];
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
-   if (popforecast==1) {
+       fprintf(ficreseij,"%9.4f", eip );
-     free_ivector(popage,0,AGESUP);
+     }
-     free_vector(popeffectif,0,AGESUP);
+     fprintf(ficreseij,"\n");
-     free_vector(popcount,0,AGESUP);
    }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   printf("\n");
-   fclose(ficrespop);
+   fprintf(ficlog,"\n");
- } /* End of popforecast */
+ }
- int fileappend(FILE *fichier, char *optionfich)
- {
+ 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[] )
-   if((fichier=fopen(optionfich,"a"))==NULL) {
-     printf("Problem with file: %s\n", optionfich);
+ {
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   /* Covariances of health expectancies eij and of total life expectancies according
-     return (0);
+    to initial status i, ei. .
-   }
+   */
-   fflush(fichier);
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   return (1);
+   int nhstepma, nstepma; /* Decreasing with age */
- }
+   double age, agelim, hf;
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
- /**************** function prwizard **********************/
+   double *xp, *xm;
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+   double **gp, **gm;
- {
+   double ***gradg, ***trgradg;
+   int theta;
-   /* Wizard to print covariance matrix template */
+   double eip, vip;
-   char ca[32], cb[32], cc[32];
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   int numlinepar;
+   xp=vector(1,npar);
+   xm=vector(1,npar);
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   for(i=1; i <=nlstate; i++){
-     jj=0;
+   pstamp(ficresstdeij);
-     for(j=1; j <=nlstate+ndeath; j++){
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-       if(j==i) continue;
+   fprintf(ficresstdeij,"# Age");
-       jj++;
+   for(i=1; i<=nlstate;i++){
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+     for(j=1; j<=nlstate;j++)
-       printf("%1d%1d",i,j);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       fprintf(ficparo,"%1d%1d",i,j);
+     fprintf(ficresstdeij," e%1d. ",i);
-       for(k=1; k<=ncovmodel;k++){
+   }
-         /*        printf(" %lf",param[i][j][k]); */
+   fprintf(ficresstdeij,"\n");
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-         printf(" 0.");
+   pstamp(ficrescveij);
-         fprintf(ficparo," 0.");
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-       }
+   fprintf(ficrescveij,"# Age");
-       printf("\n");
+   for(i=1; i<=nlstate;i++)
-       fprintf(ficparo,"\n");
+     for(j=1; j<=nlstate;j++){
-     }
+       cptj= (j-1)*nlstate+i;
-   }
+       for(i2=1; i2<=nlstate;i2++)
-   printf("# Scales (for hessian or gradient estimation)\n");
+         for(j2=1; j2<=nlstate;j2++){
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+           cptj2= (j2-1)*nlstate+i2;
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+           if(cptj2 <= cptj)
-   for(i=1; i <=nlstate; i++){
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-     jj=0;
+         }
-     for(j=1; j <=nlstate+ndeath; j++){
+     }
-       if(j==i) continue;
+   fprintf(ficrescveij,"\n");
-       jj++;
-       fprintf(ficparo,"%1d%1d",i,j);
+   if(estepm < stepm){
-       printf("%1d%1d",i,j);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       fflush(stdout);
+   }
-       for(k=1; k<=ncovmodel;k++){
+   else  hstepm=estepm;
-         /*      printf(" %le",delti3[i][j][k]); */
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+    * This is mainly to measure the difference between two models: for example
-         printf(" 0.");
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-         fprintf(ficparo," 0.");
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-       }
+    * progression in between and thus overestimating or underestimating according
-       numlinepar++;
+    * to the curvature of the survival function. If, for the same date, we
-       printf("\n");
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-       fprintf(ficparo,"\n");
+    * to compare the new estimate of Life expectancy with the same linear
-     }
+    * hypothesis. A more precise result, taking into account a more precise
-   }
+    * curvature will be obtained if estepm is as small as stepm. */
-   printf("# Covariance matrix\n");
- /* # 121 Var(a12)\n\ */
+   /* For example we decided to compute the life expectancy with the smallest unit */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+      nhstepm is the number of hstepm from age to agelim
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+      nstepm is the number of stepm from age to agelin.
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+      Look at hpijx to understand the reason of that which relies in memory size
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+      and note for a fixed period like estepm months */
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+      survival function given by stepm (the optimization length). Unfortunately it
-   fflush(stdout);
+      means that if the survival funtion is printed only each two years of age and if
-   fprintf(ficparo,"# Covariance matrix\n");
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   /* # 121 Var(a12)\n\ */
+      results. So we changed our mind and took the option of the best precision.
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   */
-   /* #   ...\n\ */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   /* If stepm=6 months */
-   for(itimes=1;itimes<=2;itimes++){
+   /* nhstepm age range expressed in number of stepm */
-     jj=0;
+   agelim=AGESUP;
-     for(i=1; i <=nlstate; i++){
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-       for(j=1; j <=nlstate+ndeath; j++){
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         if(j==i) continue;
+   /* if (stepm >= YEARM) hstepm=1;*/
-         for(k=1; k<=ncovmodel;k++){
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           jj++;
-           ca[0]= k+'a'-1;ca[1]='\0';
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           if(itimes==1){
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             printf("#%1d%1d%d",i,j,k);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-           }else{
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-             printf("%1d%1d%d",i,j,k);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
-             /*  printf(" %.5le",matcov[i][j]); */
+   for (age=bage; age<=fage; age ++){
-           }
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-           ll=0;
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-           for(li=1;li <=nlstate; li++){
+     /* if (stepm >= YEARM) hstepm=1;*/
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-               if(lj==li) continue;
-               for(lk=1;lk<=ncovmodel;lk++){
+     /* If stepm=6 months */
-                 ll++;
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-                 if(ll<=jj){
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-                   cb[0]= lk +'a'-1;cb[1]='\0';
-                   if(ll<jj){
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-                     if(itimes==1){
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     /* Computing  Variances of health expectancies */
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-                     }else{
+        decrease memory allocation */
-                       printf(" 0.");
+     for(theta=1; theta <=npar; theta++){
-                       fprintf(ficparo," 0.");
+       for(i=1; i<=npar; i++){
-                     }
+                                 xp[i] = x[i] + (i==theta ?delti[theta]:0);
-                   }else{
+                                 xm[i] = x[i] - (i==theta ?delti[theta]:0);
-                     if(itimes==1){
+       }
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-                     }else{
-                       printf(" 0.");
+       for(j=1; j<= nlstate; j++){
-                       fprintf(ficparo," 0.");
+                                 for(i=1; i<=nlstate; i++){
-                     }
+                                         for(h=0; h<=nhstepm-1; h++){
-                   }
+                                                 gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-                 }
+                                                 gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-               } /* end lk */
+                                         }
-             } /* end lj */
+                                 }
-           } /* end li */
+       }
-           printf("\n");
-           fprintf(ficparo,"\n");
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-           numlinepar++;
+                                 for(h=0; h<=nhstepm-1; h++){
-         } /* end k*/
+                                         gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-       } /*end j */
+                                 }
-     } /* end i */
+     }/* End theta */
-   } /* end itimes */
- } /* end of prwizard */
+     for(h=0; h<=nhstepm-1; h++)
- /******************* Gompertz Likelihood ******************************/
+       for(j=1; j<=nlstate*nlstate;j++)
- double gompertz(double x[])
+                                 for(theta=1; theta <=npar; theta++)
- {
+                                         trgradg[h][j][theta]=gradg[h][theta][j];
-   double A,B,L=0.0,sump=0.,num=0.;
-   int i,n=0; /* n is the size of the sample */
+                 for(ij=1;ij<=nlstate*nlstate;ij++)
-   for (i=0;i<=imx-1 ; i++) {
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-     sump=sump+weight[i];
+                                 varhe[ij][ji][(int)age] =0.;
-     /*    sump=sump+1;*/
-     num=num+1;
+                 printf("%d|",(int)age);fflush(stdout);
-   }
+                 fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+                 for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
-   /* for (i=0; i<=imx; i++)
+                                 matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-      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]);*/
+                                 matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+                                 for(ij=1;ij<=nlstate*nlstate;ij++)
-   for (i=1;i<=imx ; i++)
+                                         for(ji=1;ji<=nlstate*nlstate;ji++)
-     {
+                                                 varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-       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)
+     /* Computing expectancies */
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+                                 for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-       if (wav[i] > 1 ) { /* ??? */
+                                         eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-         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]);*/
+                                         /* 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("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+     fprintf(ficresstdeij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-   return -2*L*num/sump;
+       eip=0.;
- }
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
- /******************* Printing html file ***********/
+                                 eip += eij[i][j][(int)age];
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                                 for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-                   int lastpass, int stepm, int weightopt, char model[],\
+                                         vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-                   int imx,  double p[],double **matcov,double agemortsup){
+                                 fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-   int i,k;
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   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);
+     fprintf(ficresstdeij,"\n");
-   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(ficrescveij,"%3.0f",age );
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+     for(i=1; i<=nlstate;i++)
-   fprintf(fichtm,"</ul>");
+       for(j=1; j<=nlstate;j++){
+                                 cptj= (j-1)*nlstate+i;
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+                                 for(i2=1; i2<=nlstate;i2++)
+                                         for(j2=1; j2<=nlstate;j2++){
-  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>");
+                                                 cptj2= (j2-1)*nlstate+i2;
+                                                 if(cptj2 <= cptj)
-  for (k=agegomp;k<(agemortsup-2);k++)
+                                                         fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-    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]);
+                                         }
+       }
+     fprintf(ficrescveij,"\n");
-   fflush(fichtm);
- }
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
- /******************* Gnuplot file **************/
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   char dirfileres[132],optfileres[132];
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int ng;
+   printf("\n");
+   fprintf(ficlog,"\n");
-   /*#ifdef windows */
+   free_vector(xm,1,npar);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   free_vector(xp,1,npar);
-     /*#endif */
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-   strcpy(dirfileres,optionfilefiname);
+ }
-   strcpy(optfileres,"vpl");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+ /************ Variance ******************/
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \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(ficgp, "set ter png small\n set log y\n");
+  {
-   fprintf(ficgp, "set size 0.65,0.65\n");
+    /* Variance of health expectancies */
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+    /* double **newm;*/
- }
+    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+    /* int movingaverage(); */
+    double **dnewm,**doldm;
+    double **dnewmp,**doldmp;
+    int i, j, nhstepm, hstepm, h, nstepm ;
- /***********************************************/
+    int k;
- /**************** Main Program *****************/
+    double *xp;
- /***********************************************/
+    double **gp, **gm;  /* for var eij */
+    double ***gradg, ***trgradg; /*for var eij */
- int main(int argc, char *argv[])
+    double **gradgp, **trgradgp; /* for var p point j */
- {
+    double *gpp, *gmp; /* for var p point j */
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+    double ***p3mat;
-   int linei, month, year,iout;
+    double age,agelim, hf;
-   int jj, ll, li, lj, lk, imk;
+    /* double ***mobaverage; */
-   int numlinepar=0; /* Current linenumber of parameter file */
+    int theta;
-   int itimes;
+    char digit[4];
-   int NDIM=2;
+    char digitp[25];
-   char ca[32], cb[32], cc[32];
+    char fileresprobmorprev[FILENAMELENGTH];
-   char dummy[]="                         ";
-   /*  FILE *fichtm; *//* Html File */
+    if(popbased==1){
-   /* FILE *ficgp;*/ /*Gnuplot File */
+      if(mobilav!=0)
-   struct stat info;
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-   double agedeb, agefin,hf;
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+    }
+    else
-   double fret;
+      strcpy(digitp,"-STABLBASED_");
-   double **xi,tmp,delta;
+    /* if (mobilav!=0) { */
-   double dum; /* Dummy variable */
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   double ***p3mat;
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-   double ***mobaverage;
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-   int *indx;
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-   char line[MAXLINE], linepar[MAXLINE];
+    /*   } */
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+    /* } */
-   char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+    strcpy(fileresprobmorprev,"PRMORPREV-");
-   int firstobs=1, lastobs=10;
+    sprintf(digit,"%-d",ij);
-   int sdeb, sfin; /* Status at beginning and end */
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   int c,  h , cpt,l;
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   int ju,jl, mi;
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+    strcat(fileresprobmorprev,fileresu);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   int mobilav=0,popforecast=0;
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   int hstepm, nhstepm;
+    }
-   int agemortsup;
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   float  sumlpop=0.;
+    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+    pstamp(ficresprobmorprev);
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+    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);
-   double bage, fage, age, agelim, agebase;
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   double ftolpl=FTOL;
+      fprintf(ficresprobmorprev," p.%-d SE",j);
-   double **prlim;
+      for(i=1; i<=nlstate;i++)
-   double *severity;
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   double ***param; /* Matrix of parameters */
+    }
-   double  *p;
+    fprintf(ficresprobmorprev,"\n");
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
+    fprintf(ficgp,"\n# Routine varevsij");
-   double *delti; /* Scale */
+    fprintf(ficgp,"\nunset title \n");
-   double ***eij, ***vareij;
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   double **varpl; /* Variances of prevalence limits by age */
+    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");
-   double *epj, vepp;
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   double kk1, kk2;
+    /*   } */
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   double **ximort;
+    pstamp(ficresvij);
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   int *dcwave;
+    if(popbased==1)
+      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   char z[1]="c", occ;
+    else
+      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+    fprintf(ficresvij,"# Age");
-   char  *strt, strtend[80];
+    for(i=1; i<=nlstate;i++)
-   char *stratrunc;
+      for(j=1; j<=nlstate;j++)
-   int lstra;
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    fprintf(ficresvij,"\n");
-   long total_usecs;
+    xp=vector(1,npar);
- /*   setlocale (LC_ALL, ""); */
+    dnewm=matrix(1,nlstate,1,npar);
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+    doldm=matrix(1,nlstate,1,nlstate);
- /*   textdomain (PACKAGE); */
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
- /*   setlocale (LC_CTYPE, ""); */
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- /*   setlocale (LC_MESSAGES, ""); */
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+    gpp=vector(nlstate+1,nlstate+ndeath);
-   (void) gettimeofday(&start_time,&tzp);
+    gmp=vector(nlstate+1,nlstate+ndeath);
-   curr_time=start_time;
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   tm = *localtime(&start_time.tv_sec);
-   tmg = *gmtime(&start_time.tv_sec);
+    if(estepm < stepm){
-   strcpy(strstart,asctime(&tm));
+      printf ("Problem %d lower than %d\n",estepm, stepm);
+    }
- /*  printf("Localtime (at start)=%s",strstart); */
+    else  hstepm=estepm;
- /*  tp.tv_sec = tp.tv_sec +86400; */
+    /* For example we decided to compute the life expectancy with the smallest unit */
- /*  tm = *localtime(&start_time.tv_sec); */
+    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       nhstepm is the number of hstepm from age to agelim
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       nstepm is the number of stepm from age to agelim.
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+       Look at function hpijx to understand why because of memory size limitations,
- /*   tp.tv_sec = mktime(&tmg); */
+       we decided (b) to get a life expectancy respecting the most precise curvature of the
- /*   strt=asctime(&tmg); */
+       survival function given by stepm (the optimization length). Unfortunately it
- /*   printf("Time(after) =%s",strstart);  */
+       means that if the survival funtion is printed every two years of age and if
- /*  (void) time (&time_value);
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+       results. So we changed our mind and took the option of the best precision.
- *  tm = *localtime(&time_value);
+    */
- *  strstart=asctime(&tm);
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+    agelim = AGESUP;
- */
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   nberr=0; /* Number of errors and warnings */
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   nbwarn=0;
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   getcwd(pathcd, size);
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+      gp=matrix(0,nhstepm,1,nlstate);
-   printf("\n%s\n%s",version,fullversion);
+      gm=matrix(0,nhstepm,1,nlstate);
-   if(argc <=1){
-     printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+      for(theta=1; theta <=npar; theta++){
-     i=strlen(pathr);
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-     if(pathr[i-1]=='\n')
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       pathr[i-1]='\0';
+        }
-    for (tok = pathr; tok != NULL; ){
-       printf("Pathr |%s|\n",pathr);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-       printf("val= |%s| pathr=%s\n",val,pathr);
+        if (popbased==1) {
-       strcpy (pathtot, val);
+          if(mobilav ==0){
-       if(pathr[0] == '\0') break; /* Dirty */
+            for(i=1; i<=nlstate;i++)
-     }
+              prlim[i][i]=probs[(int)age][i][ij];
-   }
+          }else{ /* mobilav */
-   else{
+            for(i=1; i<=nlstate;i++)
-     strcpy(pathtot,argv[1]);
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-   }
+          }
-   /*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);*/
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
-   /* cutv(path,optionfile,pathtot,'\\');*/
+        for(j=1; j<= nlstate; j++){
+          for(h=0; h<=nhstepm; h++){
-   /* Split argv[0], imach program to get pathimach */
+            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-   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]); */
+        /* Next for computing probability of death (h=1 means
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+           computed over hstepm matrices product = hstepm*stepm months)
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+           as a weighted average of prlim.
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+        */
-   chdir(path); /* Can be a relative path */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
-     printf("Current directory %s!\n",pathcd);
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
-   strcpy(command,"mkdir ");
+        }
-   strcat(command,optionfilefiname);
+        /* end probability of death */
-   if((outcmd=system(command)) != 0){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     /* fclose(ficlog); */
- /*     exit(1); */
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
-   }
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+        if (popbased==1) {
- /*     perror("mkdir"); */
+          if(mobilav ==0){
- /*   } */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
-   /*-------- arguments in the command line --------*/
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
-   /* Log file */
+              prlim[i][i]=mobaverage[(int)age][i][ij];
-   strcat(filelog, optionfilefiname);
+          }
-   strcat(filelog,".log");    /* */
+        }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
-     printf("Problem with logfile %s\n",filelog);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-     goto end;
-   }
+        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+          for(h=0; h<=nhstepm; h++){
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+          }
-  path=%s \n\
+        }
-  optionfile=%s\n\
+        /* This for computing probability of death (h=1 means
-  optionfilext=%s\n\
+           computed over hstepm matrices product = hstepm*stepm months)
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+           as a weighted average of prlim.
+        */
-   printf("Local time (at start):%s",strstart);
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+          for(i=1,gmp[j]=0.; i<= nlstate; i++)
-   fflush(ficlog);
+            gmp[j] += prlim[i][i]*p3mat[i][j][1];
- /*   (void) gettimeofday(&curr_time,&tzp); */
+        }
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+        /* end probability of death */
-   /* */
+        for(j=1; j<= nlstate; j++) /* vareij */
-   strcpy(fileres,"r");
+          for(h=0; h<=nhstepm; h++){
-   strcat(fileres, optionfilefiname);
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   strcat(fileres,".txt");    /* Other files have txt extension */
+          }
-   /*---------arguments file --------*/
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+        }
-     printf("Problem with optionfile %s\n",optionfile);
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+      } /* End theta */
-     fflush(ficlog);
-     goto end;
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   }
+      for(h=0; h<=nhstepm; h++) /* veij */
+        for(j=1; j<=nlstate;j++)
+          for(theta=1; theta <=npar; theta++)
-   strcpy(filereso,"o");
+            trgradg[h][j][theta]=gradg[h][theta][j];
-   strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-     printf("Problem with Output resultfile: %s\n", filereso);
+        for(theta=1; theta <=npar; theta++)
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+          trgradgp[j][theta]=gradgp[theta][j];
-     fflush(ficlog);
-     goto end;
-   }
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+      for(i=1;i<=nlstate;i++)
-   /* Reads comments: lines beginning with '#' */
+        for(j=1;j<=nlstate;j++)
-   numlinepar=0;
+          vareij[i][j][(int)age] =0.;
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+      for(h=0;h<=nhstepm;h++){
-     fgets(line, MAXLINE, ficpar);
+        for(k=0;k<=nhstepm;k++){
-     numlinepar++;
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-     puts(line);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-     fputs(line,ficparo);
+          for(i=1;i<=nlstate;i++)
-     fputs(line,ficlog);
+            for(j=1;j<=nlstate;j++)
-   }
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-   ungetc(c,ficpar);
+        }
+      }
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-   numlinepar++;
+      /* pptj */
-   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);
+      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-   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);
+      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-   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);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
-   fflush(ficlog);
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
-   while((c=getc(ficpar))=='#' && c!= EOF){
+          varppt[j][i]=doldmp[j][i];
-     ungetc(c,ficpar);
+      /* end ppptj */
-     fgets(line, MAXLINE, ficpar);
+      /*  x centered again */
-     numlinepar++;
-     puts(line);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
+      if (popbased==1) {
-   }
+        if(mobilav ==0){
-   ungetc(c,ficpar);
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
+        }else{ /* mobilav */
-   covar=matrix(0,NCOVMAX,1,n);
+          for(i=1; i<=nlstate;i++)
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+            prlim[i][i]=mobaverage[(int)age][i][ij];
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+        }
+      }
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+      /* This for computing probability of death (h=1 means
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         computed over hstepm (estepm) matrices product = hstepm*stepm months)
+         as a weighted average of prlim.
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+      */
-   delti=delti3[1][1];
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+      for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+        for(i=1,gmp[j]=0.;i<= nlstate; i++)
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+      }
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+      /* end probability of death */
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     fclose (ficparo);
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     fclose (ficlog);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     goto end;
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-     exit(0);
+        for(i=1; i<=nlstate;i++){
-   }
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-   else if(mle==-3) {
+        }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+      }
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+      fprintf(ficresprobmorprev,"\n");
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+      fprintf(ficresvij,"%.0f ",age );
-     matcov=matrix(1,npar,1,npar);
+      for(i=1; i<=nlstate;i++)
-   }
+        for(j=1; j<=nlstate;j++){
-   else{
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-     /* Read guess parameters */
+        }
-     /* Reads comments: lines beginning with '#' */
+      fprintf(ficresvij,"\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      free_matrix(gp,0,nhstepm,1,nlstate);
-       ungetc(c,ficpar);
+      free_matrix(gm,0,nhstepm,1,nlstate);
-       fgets(line, MAXLINE, ficpar);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-       numlinepar++;
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-       puts(line);
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fputs(line,ficparo);
+    } /* End age */
-       fputs(line,ficlog);
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
-     }
+    free_vector(gmp,nlstate+1,nlstate+ndeath);
-     ungetc(c,ficpar);
+    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-     for(i=1; i <=nlstate; i++){
+    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
-       j=0;
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-         if(jj==i) continue;
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-         j++;
+    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         if ((i1 != i) && (j1 != j)){
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
- It might be a problem of design; if ncovcol and the model are correct\n \
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-           exit(1);
+    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(ficparo,"%1d%1d",i1,j1);
+    /*  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);
-         if(mle==1)
+     */
-           printf("%1d%1d",i,j);
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-         fprintf(ficlog,"%1d%1d",i,j);
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-         for(k=1; k<=ncovmodel;k++){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+    free_vector(xp,1,npar);
-           if(mle==1){
+    free_matrix(doldm,1,nlstate,1,nlstate);
-             printf(" %lf",param[i][j][k]);
+    free_matrix(dnewm,1,nlstate,1,npar);
-             fprintf(ficlog," %lf",param[i][j][k]);
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           }
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-           else
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-             fprintf(ficlog," %lf",param[i][j][k]);
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-           fprintf(ficparo," %lf",param[i][j][k]);
+    fclose(ficresprobmorprev);
-         }
+    fflush(ficgp);
-         fscanf(ficpar,"\n");
+    fflush(fichtm);
-         numlinepar++;
+  }  /* end varevsij */
-         if(mle==1)
-           printf("\n");
+ /************ Variance of prevlim ******************/
-         fprintf(ficlog,"\n");
+  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[])
-         fprintf(ficparo,"\n");
+ {
-       }
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-     }
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-     fflush(ficlog);
+   double **dnewm,**doldm;
-     p=param[1][1];
+   int i, j, nhstepm, hstepm;
+   double *xp;
-     /* Reads comments: lines beginning with '#' */
+   double *gp, *gm;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   double **gradg, **trgradg;
-       ungetc(c,ficpar);
+   double **mgm, **mgp;
-       fgets(line, MAXLINE, ficpar);
+   double age,agelim;
-       numlinepar++;
+   int theta;
-       puts(line);
-       fputs(line,ficparo);
+   pstamp(ficresvpl);
-       fputs(line,ficlog);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-     }
+   fprintf(ficresvpl,"# Age");
-     ungetc(c,ficpar);
+   for(i=1; i<=nlstate;i++)
+       fprintf(ficresvpl," %1d-%1d",i,i);
-     for(i=1; i <=nlstate; i++){
+   fprintf(ficresvpl,"\n");
-       for(j=1; j <=nlstate+ndeath-1; j++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   xp=vector(1,npar);
-         if ((i1-i)*(j1-j)!=0){
+   dnewm=matrix(1,nlstate,1,npar);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+   doldm=matrix(1,nlstate,1,nlstate);
-           exit(1);
-         }
+   hstepm=1*YEARM; /* Every year of age */
-         printf("%1d%1d",i,j);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-         fprintf(ficparo,"%1d%1d",i1,j1);
+   agelim = AGESUP;
-         fprintf(ficlog,"%1d%1d",i1,j1);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         for(k=1; k<=ncovmodel;k++){
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+     if (stepm >= YEARM) hstepm=1;
-           printf(" %le",delti3[i][j][k]);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           fprintf(ficparo," %le",delti3[i][j][k]);
+     gradg=matrix(1,npar,1,nlstate);
-           fprintf(ficlog," %le",delti3[i][j][k]);
+     mgp=matrix(1,npar,1,nlstate);
-         }
+     mgm=matrix(1,npar,1,nlstate);
-         fscanf(ficpar,"\n");
+     gp=vector(1,nlstate);
-         numlinepar++;
+     gm=vector(1,nlstate);
-         printf("\n");
-         fprintf(ficparo,"\n");
+     for(theta=1; theta <=npar; theta++){
-         fprintf(ficlog,"\n");
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-       }
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     }
+       }
-     fflush(ficlog);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-     delti=delti3[1][1];
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       for(i=1;i<=nlstate;i++){
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+         gp[i] = prlim[i][i];
+         mgp[theta][i] = prlim[i][i];
-     /* Reads comments: lines beginning with '#' */
+       }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       for(i=1; i<=npar; i++) /* Computes gradient */
-       ungetc(c,ficpar);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       fgets(line, MAXLINE, ficpar);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       numlinepar++;
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       puts(line);
+       else
-       fputs(line,ficparo);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       fputs(line,ficlog);
+       for(i=1;i<=nlstate;i++){
-     }
+         gm[i] = prlim[i][i];
-     ungetc(c,ficpar);
+         mgm[theta][i] = prlim[i][i];
+       }
-     matcov=matrix(1,npar,1,npar);
+       for(i=1;i<=nlstate;i++)
-     for(i=1; i <=npar; i++){
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-       fscanf(ficpar,"%s",&str);
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
-       if(mle==1)
+     } /* End theta */
-         printf("%s",str);
-       fprintf(ficlog,"%s",str);
+     trgradg =matrix(1,nlstate,1,npar);
-       fprintf(ficparo,"%s",str);
-       for(j=1; j <=i; j++){
+     for(j=1; j<=nlstate;j++)
-         fscanf(ficpar," %le",&matcov[i][j]);
+       for(theta=1; theta <=npar; theta++)
-         if(mle==1){
+         trgradg[j][theta]=gradg[theta][j];
-           printf(" %.5le",matcov[i][j]);
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-         }
+     /*   printf("\nmgm mgp %d ",(int)age); */
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     /*   for(j=1; j<=nlstate;j++){ */
-         fprintf(ficparo," %.5le",matcov[i][j]);
+     /*  printf(" %d ",j); */
-       }
+     /*  for(theta=1; theta <=npar; theta++) */
-       fscanf(ficpar,"\n");
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
-       numlinepar++;
+     /*  printf("\n "); */
-       if(mle==1)
+     /*   } */
-         printf("\n");
+     /* } */
-       fprintf(ficlog,"\n");
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-       fprintf(ficparo,"\n");
+     /*   printf("\n gradg %d ",(int)age); */
-     }
+     /*   for(j=1; j<=nlstate;j++){ */
-     for(i=1; i <=npar; i++)
+     /*  printf("%d ",j); */
-       for(j=i+1;j<=npar;j++)
+     /*  for(theta=1; theta <=npar; theta++) */
-         matcov[i][j]=matcov[j][i];
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
-     if(mle==1)
+     /*   } */
-       printf("\n");
+     /* } */
-     fprintf(ficlog,"\n");
+     for(i=1;i<=nlstate;i++)
-     fflush(ficlog);
+       varpl[i][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-     /*-------- Rewriting parameter file ----------*/
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     }else{
-     strcat(rfileres,".");    /* */
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+     }
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+     for(i=1;i<=nlstate;i++)
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-     }
-     fprintf(ficres,"#%s\n",version);
+     fprintf(ficresvpl,"%.0f ",age );
-   }    /* End of mle != -3 */
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-   /*-------- data file ----------*/
+     fprintf(ficresvpl,"\n");
-   if((fic=fopen(datafile,"r"))==NULL)    {
+     free_vector(gp,1,nlstate);
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+     free_vector(gm,1,nlstate);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+     free_matrix(mgm,1,npar,1,nlstate);
-   }
+     free_matrix(mgp,1,npar,1,nlstate);
+     free_matrix(gradg,1,npar,1,nlstate);
-   n= lastobs;
+     free_matrix(trgradg,1,nlstate,1,npar);
-   severity = vector(1,maxwav);
+   } /* End age */
-   outcome=imatrix(1,maxwav+1,1,n);
-   num=lvector(1,n);
+   free_vector(xp,1,npar);
-   moisnais=vector(1,n);
+   free_matrix(doldm,1,nlstate,1,npar);
-   annais=vector(1,n);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+ }
-   agedc=vector(1,n);
-   cod=ivector(1,n);
+ /************ Variance of one-step probabilities  ******************/
-   weight=vector(1,n);
+ 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[])
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ {
-   mint=matrix(1,maxwav,1,n);
+   int i, j=0,  k1, l1, tj;
-   anint=matrix(1,maxwav,1,n);
+   int k2, l2, j1,  z1;
-   s=imatrix(1,maxwav+1,1,n);
+   int k=0, l;
-   tab=ivector(1,NCOVMAX);
+   int first=1, first1, first2;
-   ncodemax=ivector(1,8);
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   double **dnewm,**doldm;
-   i=1;
+   double *xp;
-   linei=0;
+   double *gp, *gm;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+   double **gradg, **trgradg;
-     linei=linei+1;
+   double **mu;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+   double age, cov[NCOVMAX+1];
-       if(line[j] == '\t')
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-         line[j] = ' ';
+   int theta;
-     }
+   char fileresprob[FILENAMELENGTH];
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   char fileresprobcov[FILENAMELENGTH];
-       ;
+   char fileresprobcor[FILENAMELENGTH];
-     };
+   double ***varpij;
-     line[j+1]=0;  /* Trims blanks at end of line */
-     if(line[0]=='#'){
+   strcpy(fileresprob,"PROB_");
-       fprintf(ficlog,"Comment line\n%s\n",line);
+   strcat(fileresprob,fileres);
-       printf("Comment line\n%s\n",line);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-       continue;
+     printf("Problem with resultfile: %s\n", fileresprob);
-     }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   }
-     for (j=maxwav;j>=1;j--){
+   strcpy(fileresprobcov,"PROBCOV_");
-       cutv(stra, strb,line,' ');
+   strcat(fileresprobcov,fileresu);
-       errno=0;
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-       lval=strtol(strb,&endptr,10);
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   }
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+   strcpy(fileresprobcor,"PROBCOR_");
-         exit(1);
+   strcat(fileresprobcor,fileresu);
-       }
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-       s[j][i]=lval;
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-       strcpy(line,stra);
+   }
-       cutv(stra, strb,line,' ');
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-       }
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-       else  if(iout=sscanf(strb,"%s.") != 0){
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-         month=99;
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-         year=9999;
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-       }else{
+   pstamp(ficresprob);
-         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);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-         exit(1);
+   fprintf(ficresprob,"# Age");
-       }
+   pstamp(ficresprobcov);
-       anint[j][i]= (double) year;
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-       mint[j][i]= (double)month;
+   fprintf(ficresprobcov,"# Age");
-       strcpy(line,stra);
+   pstamp(ficresprobcor);
-     } /* ENd Waves */
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcor,"# Age");
-     cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     }
+   for(i=1; i<=nlstate;i++)
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+     for(j=1; j<=(nlstate+ndeath);j++){
-       month=99;
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       year=9999;
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-     }else{
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+     }
-       exit(1);
+  /* fprintf(ficresprob,"\n");
-     }
+   fprintf(ficresprobcov,"\n");
-     andc[i]=(double) year;
+   fprintf(ficresprobcor,"\n");
-     moisdc[i]=(double) month;
+  */
-     strcpy(line,stra);
+   xp=vector(1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-     cutv(stra, strb,line,' ');
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-     }
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-     else  if(iout=sscanf(strb,"%s.") != 0){
+   first=1;
-       month=99;
+   fprintf(ficgp,"\n# Routine varprob");
-       year=9999;
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-     }else{
+   fprintf(fichtm,"\n");
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
-       exit(1);
+   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);
-     annais[i]=(double)(year);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-     moisnais[i]=(double)(month);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-     strcpy(line,stra);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-     cutv(stra, strb,line,' ');
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-     errno=0;
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-     dval=strtod(strb,&endptr);
+ standard deviations wide on each axis. <br>\
-     if( strb[0]=='\0' || (*endptr != '\0')){
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-       exit(1);
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-     }
-     weight[i]=dval;
+   cov[1]=1;
-     strcpy(line,stra);
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
-     for (j=ncovcol;j>=1;j--){
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-       cutv(stra, strb,line,' ');
+   j1=0;
-       errno=0;
+   for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */
-       lval=strtol(strb,&endptr,10);
+                 if  (cptcovn>0) {
-       if( strb[0]=='\0' || (*endptr != '\0')){
+                         fprintf(ficresprob, "\n#********** Variable ");
-         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);
+                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         exit(1);
+                         fprintf(ficresprob, "**********\n#\n");
-       }
+                         fprintf(ficresprobcov, "\n#********** Variable ");
-       if(lval <-1 || lval >1){
+                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+                         fprintf(ficresprobcov, "**********\n#\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 \
+                         fprintf(ficgp, "\n#********** Variable ");
-  For example, for multinomial values like 1, 2 and 3,\n \
+                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-  build V1=0 V2=0 for the reference value (1),\n \
+                         fprintf(ficgp, "**********\n#\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 \
+                         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-  Exiting.\n",lval,linei, i,line,j);
+                         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         exit(1);
+                         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-       }
-       covar[j][i]=(double)(lval);
+                         fprintf(ficresprobcor, "\n#********** Variable ");
-       strcpy(line,stra);
+                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     }
+                         fprintf(ficresprobcor, "**********\n#");
-     lstra=strlen(stra);
+                         if(invalidvarcomb[j1]){
+                           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+                           fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
-       stratrunc = &(stra[lstra-9]);
+                           continue;
-       num[i]=atol(stratrunc);
+                         }
-     }
+                 }
-     else
+                 gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       num[i]=atol(stra);
+                 trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+                 gp=vector(1,(nlstate)*(nlstate+ndeath));
-       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;}*/
+                 gm=vector(1,(nlstate)*(nlstate+ndeath));
+                 for (age=bage; age<=fage; age ++){
-     i=i+1;
+                         cov[2]=age;
-   } /* End loop reading  data */
+                         if(nagesqr==1)
-   fclose(fic);
+                                 cov[3]= age*age;
-   /* printf("ii=%d", ij);
+                         for (k=1; k<=cptcovn;k++) {
-      scanf("%d",i);*/
+                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-   imx=i-1; /* Number of individuals */
+                                 /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
+                                                                                                                                                                                                                                                                          * 1  1 1 1 1
-   /* for (i=1; i<=imx; i++){
+                                                                                                                                                                                                                                                                          * 2  2 1 1 1
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+                                                                                                                                                                                                                                                                          * 3  1 2 1 1
-     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;
+                                 /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-     }*/
+                         }
-    /*  for (i=1; i<=imx; i++){
+                         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-      if (s[4][i]==9)  s[4][i]=-1;
+                         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-      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 (k=1; k<=cptcovprod;k++)
+                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-   /* for (i=1; i<=imx; i++) */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+                         for(theta=1; theta <=npar; theta++){
-      else weight[i]=1;*/
+                                 for(i=1; i<=npar; i++)
+                                         xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-   /* Calculation of the number of parameters from char model */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   Tprod=ivector(1,15);
-   Tvaraff=ivector(1,15);
+                                 k=0;
-   Tvard=imatrix(1,15,1,2);
+                                 for(i=1; i<= (nlstate); i++){
-   Tage=ivector(1,15);
+                                         for(j=1; j<=(nlstate+ndeath);j++){
+                                                 k=k+1;
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+                                                 gp[k]=pmmij[i][j];
-     j=0, j1=0, k1=1, k2=1;
+                                         }
-     j=nbocc(model,'+'); /* j=Number of '+' */
+                                 }
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
-     cptcovn=j+1;
+                                 for(i=1; i<=npar; i++)
-     cptcovprod=j1; /*Number of products */
+                                         xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-     strcpy(modelsav,model);
+                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+                                 k=0;
-       printf("Error. Non available option model=%s ",model);
+                                 for(i=1; i<=(nlstate); i++){
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+                                         for(j=1; j<=(nlstate+ndeath);j++){
-       goto end;
+                                                 k=k+1;
-     }
+                                                 gm[k]=pmmij[i][j];
+                                         }
-     /* This loop fills the array Tvar from the string 'model'.*/
+                                 }
-     for(i=(j+1); i>=1;i--){
+                                 for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+                                         gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-       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);*/
+                         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-       if (strchr(strb,'*')) {  /* Model includes a product */
+                                 for(theta=1; theta <=npar; theta++)
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+                                         trgradg[j][theta]=gradg[theta][j];
-         if (strcmp(strc,"age")==0) { /* Vn*age */
-           cptcovprod--;
+                         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-           cutv(strb,stre,strd,'V');
+                         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
-           cptcovage++;
+                         pmij(pmmij,cov,ncovmodel,x,nlstate);
-             Tage[cptcovage]=i;
-             /*printf("stre=%s ", stre);*/
+                         k=0;
-         }
+                         for(i=1; i<=(nlstate); i++){
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+                                 for(j=1; j<=(nlstate+ndeath);j++){
-           cptcovprod--;
+                                         k=k+1;
-           cutv(strb,stre,strc,'V');
+                                         mu[k][(int) age]=pmmij[i][j];
-           Tvar[i]=atoi(stre);
+                                 }
-           cptcovage++;
+                         }
-           Tage[cptcovage]=i;
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-         }
+                                 for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-         else {  /* Age is not in the model */
+                                         varpij[i][j][(int)age] = doldm[i][j];
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
+                         /*printf("\n%d ",(int)age);
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+                                 for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           Tprod[k1]=i;
+                                 printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           Tvard[k1][1]=atoi(strc); /* m*/
+                                 fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           Tvard[k1][2]=atoi(stre); /* n */
+                                 }*/
-           Tvar[cptcovn+k2]=Tvard[k1][1];
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+                         fprintf(ficresprob,"\n%d ",(int)age);
-           for (k=1; k<=lastobs;k++)
+                         fprintf(ficresprobcov,"\n%d ",(int)age);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+                         fprintf(ficresprobcor,"\n%d ",(int)age);
-           k1++;
-           k2=k2+2;
+                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-         }
+                                 fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-       }
+                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       else { /* no more sum */
+                                 fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+                                 fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-        /*  scanf("%d",i);*/
+                         }
-       cutv(strd,strc,strb,'V');
+                         i=0;
-       Tvar[i]=atoi(strc);
+                         for (k=1; k<=(nlstate);k++){
-       }
+                                 for (l=1; l<=(nlstate+ndeath);l++){
-       strcpy(modelsav,stra);
+                                         i++;
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+                                         fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-         scanf("%d",i);*/
+                                         fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-     } /* end of loop + */
+                                         for (j=1; j<=i;j++){
-   } /* end model */
+                                                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
+                                                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-   /*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(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-     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]);
+                         }/* end of loop for state */
-   printf("cptcovprod=%d ", cptcovprod);
+                 } /* end of loop for age */
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+                 free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+                 free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   scanf("%d ",i);*/
+                 free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+                 free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-     /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+                 /* Confidence intervalle of pij  */
-     for(i=1;i<=n;i++) weight[i]=1.0;
+                 /*
-   }
+                         fprintf(ficgp,"\nunset parametric;unset label");
-     /*-calculation of age at interview from date of interview and age at death -*/
+                         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   agev=matrix(1,maxwav,1,imx);
+                         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-   for (i=1; i<=imx; i++) {
+                         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-     for(m=2; (m<= maxwav); m++) {
+                         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+                         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-         anint[m][i]=9999;
+                 */
-         s[m][i]=-1;
-       }
+                 /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+                 first1=1;first2=2;
-         nberr++;
+                 for (k2=1; k2<=(nlstate);k2++){
-         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);
+                         for (l2=1; l2<=(nlstate+ndeath);l2++){
-         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);
+                                 if(l2==k2) continue;
-         s[m][i]=-1;
+                                 j=(k2-1)*(nlstate+ndeath)+l2;
-       }
+                                 for (k1=1; k1<=(nlstate);k1++){
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+                                         for (l1=1; l1<=(nlstate+ndeath);l1++){
-         nberr++;
+                                                 if(l1==k1) continue;
-         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]);
+                                                 i=(k1-1)*(nlstate+ndeath)+l1;
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+                                                 if(i<=j) continue;
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+                                                 for (age=bage; age<=fage; age ++){
-       }
+                                                         if ((int)age %5==0){
-     }
+                                                                 v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-   }
+                                                                 v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                                                                 cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-   for (i=1; i<=imx; i++)  {
+                                                                 mu1=mu[i][(int) age]/stepm*YEARM ;
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+                                                                 mu2=mu[j][(int) age]/stepm*YEARM;
-     for(m=firstpass; (m<= lastpass); m++){
+                                                                 c12=cv12/sqrt(v1*v2);
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+                                                                 /* Computing eigen value of matrix of covariance */
-         if (s[m][i] >= nlstate+1) {
+                                                                 lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-           if(agedc[i]>0)
+                                                                 lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+                                                                 if ((lc2 <0) || (lc1 <0) ){
-               agev[m][i]=agedc[i];
+                                                                         if(first2==1){
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+                                                                                 first1=0;
-             else {
+                                                                                 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);
-               if ((int)andc[i]!=9999){
+                                                                         }
-                 nbwarn++;
+                                                                         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);
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                                                                         /* lc1=fabs(lc1); */ /* If we want to have them positive */
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                                                                         /* lc2=fabs(lc2); */
-                 agev[m][i]=-1;
+                                                                 }
-               }
-             }
+                                                                 /* Eigen vectors */
-         }
+                                                                 v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                                                 /*v21=sqrt(1.-v11*v11); *//* error */
-                                  years but with the precision of a month */
+                                                                 v21=(lc1-v1)/cv12*v11;
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+                                                                 v12=-v21;
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+                                                                 v22=v11;
-             agev[m][i]=1;
+                                                                 tnalp=v21/v11;
-           else if(agev[m][i] <agemin){
+                                                                 if(first1==1){
-             agemin=agev[m][i];
+                                                                         first1=0;
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+                                                                         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);
-           }
+                                                                 }
-           else if(agev[m][i] >agemax){
+                                                                 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);
-             agemax=agev[m][i];
+                                                                 /*printf(fignu*/
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+                                                                 /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-           }
+                                                                 /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+                                                                 if(first==1){
-           /*     agev[m][i] = age[i]+2*m;*/
+                                                                         first=0;
-         }
+                                                                         fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
-         else { /* =9 */
+                                                                         fprintf(ficgp,"\nset parametric;unset label");
-           agev[m][i]=1;
+                                                                         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);
-           s[m][i]=-1;
+                                                                         fprintf(ficgp,"\nset ter svg size 640, 480");
-         }
+                                                                         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.svg\">                                                                                                                                           \
-       else /*= 0 Unknown */
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
-         agev[m][i]=1;
+                                                                                                         subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
-     }
+                                                                                                         subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                                                                         fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-   }
+                                                                         fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-   for (i=1; i<=imx; i++)  {
+                                                                         fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-     for(m=firstpass; (m<=lastpass); m++){
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-       if (s[m][i] > (nlstate+ndeath)) {
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-         nberr++;
+                     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",     \
-         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);
+                                                                 mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                            \
-         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);
+                                                                 mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-         goto end;
+                                                                 }else{
-       }
+                                                                         first=0;
-     }
+                                                                         fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-   }
+                                                                         fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                                                                         fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   /*for (i=1; i<=imx; i++){
+                                                                         fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
-   for (m=firstpass; (m<lastpass); m++){
+                                                                                                         mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                    \
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+                                                                                                         mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- }
+                                                                 }/* if first */
+                                                         } /* age mod 5 */
- }*/
+                                                 } /* end loop age */
+                                                 fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                                                 first=1;
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+                                         } /*l12 */
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+                                 } /* k12 */
+                         } /*l1 */
-   agegomp=(int)agemin;
+                 }/* k1 */
-   free_vector(severity,1,maxwav);
+         }  /* loop on combination of covariates j1 */
-   free_imatrix(outcome,1,maxwav+1,1,n);
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   free_vector(moisnais,1,n);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   free_vector(annais,1,n);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   /* free_matrix(mint,1,maxwav,1,n);
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-      free_matrix(anint,1,maxwav,1,n);*/
+   free_vector(xp,1,npar);
-   free_vector(moisdc,1,n);
+   fclose(ficresprob);
-   free_vector(andc,1,n);
+   fclose(ficresprobcov);
+   fclose(ficresprobcor);
+   fflush(ficgp);
-   wav=ivector(1,imx);
+   fflush(fichtmcov);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+ }
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+ /******************* Printing html file ***********/
-   /* Concatenates waves */
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+                   int popforecast, int prevfcast, int backcast, int estepm , \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, \
-   Tcode=ivector(1,100);
+                   double jprev2, double mprev2,double anprev2, double dateprev2){
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   int jj1, k1, i1, cpt;
-   ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+    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 \
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+ </ul>");
-                                  the estimations*/
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
-   h=0;
+    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",
-   m=pow(2,cptcoveff);
+            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) ",
-   for(k=1;k<=cptcoveff; k++){
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
-     for(i=1; i <=(m/pow(2,k));i++){
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
-       for(j=1; j <= ncodemax[k]; j++){
+    fprintf(fichtm,"\
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-           h++;
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+    fprintf(fichtm,"\
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-         }
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
-       }
+    fprintf(fichtm,"\
-     }
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-   }
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+    fprintf(fichtm,"\
-      codtab[1][2]=1;codtab[2][2]=2; */
+  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-   /* for(i=1; i <=m ;i++){
+            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
-      for(k=1; k <=cptcovn; k++){
+    fprintf(fichtm,"\
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-      }
+    <a href=\"%s\">%s</a> <br>\n",
-      printf("\n");
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
-      }
+    if(prevfcast==1){
-      scanf("%d",i);*/
+      fprintf(fichtm,"\
+  - Prevalence projections by age and states:                            \
-   /*------------ gnuplot -------------*/
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
-   strcpy(optionfilegnuplot,optionfilefiname);
+    }
-   if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   strcat(optionfilegnuplot,".gp");
+  m=pow(2,cptcoveff);
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-     printf("Problem with file %s",optionfilegnuplot);
-   }
+  jj1=0;
-   else{
+  for(k1=1; k1<=m;k1++){
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-     fprintf(ficgp,"set missing 'NaNq'\n");
+          jj1++;
-   }
+          if (cptcovn > 0) {
-   /*  fclose(ficgp);*/
+                  fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   /*--------- index.htm --------*/
+                  for (cpt=1; cpt<=cptcoveff;cpt++){
+                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+                          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
-   if(mle==-3)
+                  }
-     strcat(optionfilehtm,"-mort");
+                  fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   strcat(optionfilehtm,".htm");
+                  if(invalidvarcomb[k1]){
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+                          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+                          printf("\nCombination (%d) ignored because no cases \n",k1);
-   }
+                          continue;
+                  }
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+          }
-   strcat(optionfilehtmcov,"-cov.htm");
+          /* aij, bij */
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+          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> \
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+ <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-   }
+          /* Pij */
-   else{
+          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> \
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+          /* Quasi-incidences */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+          fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
-   }
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+          /* Survival functions (period) in state j */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+          for(cpt=1; cpt<=nlstate;cpt++){
- \n\
+                  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> \
- <hr  size=\"2\" color=\"#EC5E5E\">\
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
-  <ul><li><h4>Parameter files</h4>\n\
+          }
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+          /* State specific survival functions (period) */
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+          for(cpt=1; cpt<=nlstate;cpt++){
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+                  fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
-  - Date and time at start: %s</ul>\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);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+          }
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+          /* Period (stable) prevalence in each health state */
-           fileres,fileres,\
+          for(cpt=1; cpt<=nlstate;cpt++){
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+                  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> \
-   fflush(fichtm);
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+          }
-   strcpy(pathr,path);
+          if(backcast==1){
-   strcat(pathr,optionfilefiname);
+      /* Period (stable) back prevalence in each health state */
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        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> \
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
-      and prints on file fileres'p'. */
+      }
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+          }
+          if(prevfcast==1){
-   fprintf(fichtm,"\n");
+                  /* Projection of prevalence up to period (stable) prevalence in each health state */
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+                  for(cpt=1; cpt<=nlstate;cpt++){
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+                          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> \
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\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);
-           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 */
+          for(cpt=1; cpt<=nlstate;cpt++) {
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                  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> \
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+ <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
+          }
+    /* } /\* end i1 *\/ */
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+  }/* End k1 */
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+  fprintf(fichtm,"</ul>");
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+  fprintf(fichtm,"\
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
-   if (mle==-3){
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
-     ximort=matrix(1,NDIM,1,NDIM);
+ But because parameters are usually highly correlated (a higher incidence of disability \
-     cens=ivector(1,n);
+ and a higher incidence of recovery can give very close observed transition) it might \
-     ageexmed=vector(1,n);
+ be very useful to look not only at linear confidence intervals estimated from the \
-     agecens=vector(1,n);
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
-     dcwave=ivector(1,n);
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
+ covariance matrix of the one-step probabilities. \
-     for (i=1; i<=imx; i++){
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-       dcwave[i]=-1;
-       for (m=firstpass; m<=lastpass; m++)
+  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-         if (s[m][i]>nlstate) {
+          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-           dcwave[i]=m;
+  fprintf(fichtm,"\
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-           break;
+          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-         }
-     }
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     for (i=1; i<=imx; i++) {
+          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-       if (wav[i]>0){
+  fprintf(fichtm,"\
-         ageexmed[i]=agev[mw[1][i]][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): \
-         j=wav[i];
+    <a href=\"%s\">%s</a> <br>\n</li>",
-         agecens[i]=1.;
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
+  fprintf(fichtm,"\
-         if (ageexmed[i]> 1 && wav[i] > 0){
+  - (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): \
-           agecens[i]=agev[mw[j][i]][i];
+    <a href=\"%s\">%s</a> <br>\n</li>",
-           cens[i]= 1;
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-         }else if (ageexmed[i]< 1)
+  fprintf(fichtm,"\
-           cens[i]= -1;
+  - 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",
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-           cens[i]=0 ;
+  fprintf(fichtm,"\
-       }
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-       else cens[i]=-1;
+          estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-     }
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-     for (i=1;i<=NDIM;i++) {
+          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
-       for (j=1;j<=NDIM;j++)
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-     }
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-     p[1]=0.0268; p[NDIM]=0.083;
+ /*      <br>",fileres,fileres,fileres,fileres); */
-     /*printf("%lf %lf", p[1], p[2]);*/
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+  fflush(fichtm);
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
+  m=pow(2,cptcoveff);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-       printf("Problem with resultfile: %s\n", filerespow);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+  jj1=0;
-     }
+  for(k1=1; k1<=m;k1++){
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-     /*  for (i=1;i<=nlstate;i++)
+                  jj1++;
-         for(j=1;j<=nlstate+ndeath;j++)
+      if (cptcovn > 0) {
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-     */
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-     fprintf(ficrespow,"\n");
+                                                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-     fclose(ficrespow);
+                          if(invalidvarcomb[k1]){
+                                  fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+                                  continue;
+                          }
-     for(i=1; i <=NDIM; i++)
+      }
-       for(j=i+1;j<=NDIM;j++)
+      for(cpt=1; cpt<=nlstate;cpt++) {
-         matcov[i][j]=matcov[j][i];
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
-     printf("\nCovariance matrix\n ");
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
-     for(i=1; i <=NDIM; i++) {
+      }
-       for(j=1;j<=NDIM;j++){
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-         printf("%f ",matcov[i][j]);
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-       }
+ true period expectancies (those weighted with period prevalences are also\
-       printf("\n ");
+  drawn in addition to the population based expectancies computed using\
-     }
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+    /* } /\* end i1 *\/ */
-     for (i=1;i<=NDIM;i++)
+  }/* End k1 */
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+  fprintf(fichtm,"</ul>");
+  fflush(fichtm);
-     lsurv=vector(1,AGESUP);
+ }
-     lpop=vector(1,AGESUP);
-     tpop=vector(1,AGESUP);
+ /******************* Gnuplot file **************/
-     lsurv[agegomp]=100000;
+  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
-     for (k=agegomp;k<=AGESUP;k++) {
+   char dirfileres[132],optfileres[132];
-       agemortsup=k;
+         char gplotcondition[132];
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-     }
+   int lv=0, vlv=0, kl=0;
+   int ng=0;
-     for (k=agegomp;k<agemortsup;k++)
+   int vpopbased;
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+         int ioffset; /* variable offset for columns */
-     for (k=agegomp;k<agemortsup;k++){
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       sumlpop=sumlpop+lpop[k];
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     }
+ /*   } */
-     tpop[agegomp]=sumlpop;
+   /*#ifdef windows */
-     for (k=agegomp;k<(agemortsup-3);k++){
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-       /*  tpop[k+1]=2;*/
+     /*#endif */
-       tpop[k+1]=tpop[k]-lpop[k];
+   m=pow(2,cptcoveff);
-     }
+   /* Contribution to likelihood */
+   /* Plot the probability implied in the likelihood */
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
-     for (k=agegomp;k<(agemortsup-2);k++)
+     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
-       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+ /* nice for mle=4 plot by number of matrix products.
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
-                      stepm, weightopt,\
+     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));
-                      model,imx,p,matcov,agemortsup);
+     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));
-     free_vector(lsurv,1,AGESUP);
+     for (i=1; i<= nlstate ; i ++) {
-     free_vector(lpop,1,AGESUP);
+       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
-     free_vector(tpop,1,AGESUP);
+       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
-   } /* Endof if mle==-3 */
+       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+       for (j=2; j<= nlstate+ndeath ; j ++) {
-   else{ /* For mle >=1 */
+                                 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);
+       }
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+       fprintf(ficgp,";\nset out; unset ylabel;\n");
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     }
-     for (k=1; k<=npar;k++)
+     /* 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(" %d %8.5f",k,p[k]);
+     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
-     printf("\n");
+     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
-     globpr=1; /* to print the contributions */
+     fprintf(ficgp,"\nset out;unset log\n");
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+   strcpy(dirfileres,optionfilefiname);
-       printf(" %d %8.5f",k,p[k]);
+   strcpy(optfileres,"vpl");
-     printf("\n");
+  /* 1eme*/
-     if(mle>=1){ /* Could be 1 or 2 */
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
-     }
+       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
-     /*--------- results files --------------*/
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-     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);
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                                 vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-     for(i=1,jk=1; i <=nlstate; i++){
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       for(k=1; k <=(nlstate+ndeath); k++){
+       }
-         if (k != i) {
+       fprintf(ficgp,"\n#\n");
-           printf("%d%d ",i,k);
+                         if(invalidvarcomb[k1]){
-           fprintf(ficlog,"%d%d ",i,k);
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-           fprintf(ficres,"%1d%1d ",i,k);
+                                                 continue;
-           for(j=1; j <=ncovmodel; j++){
+                         }
-             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+                         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
-             fprintf(ficres,"%lf ",p[jk]);
+                         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
-             jk++;
+                         fprintf(ficgp,"set xlabel \"Age\" \n\
-           }
+ set ylabel \"Probability\" \n   \
-           printf("\n");
+ set ter svg size 640, 480\n     \
-           fprintf(ficlog,"\n");
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-           fprintf(ficres,"\n");
-         }
+                         for (i=1; i<= nlstate ; i ++) {
-       }
+                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     }
+                                 else        fprintf(ficgp," %%*lf (%%*lf)");
-     if(mle!=0){
+                         }
-       /* Computing hessian and covariance matrix */
+                         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);
-       ftolhess=ftol; /* Usually correct */
+                         for (i=1; i<= nlstate ; i ++) {
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     }
+                                 else fprintf(ficgp," %%*lf (%%*lf)");
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+                         }
-     printf("# Scales (for hessian or gradient estimation)\n");
+                         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+                         for (i=1; i<= nlstate ; i ++) {
-     for(i=1,jk=1; i <=nlstate; i++){
+                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       for(j=1; j <=nlstate+ndeath; j++){
+                                 else fprintf(ficgp," %%*lf (%%*lf)");
-         if (j!=i) {
+                         }
-           fprintf(ficres,"%1d%1d",i,j);
+                         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-           printf("%1d%1d",i,j);
+                         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
-           fprintf(ficlog,"%1d%1d",i,j);
+                                 /* 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); */
-           for(k=1; k<=ncovmodel;k++){
+                                 fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
-             printf(" %.5e",delti[jk]);
+                                 kl=0;
-             fprintf(ficlog," %.5e",delti[jk]);
+                                 for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             fprintf(ficres," %.5e",delti[jk]);
+                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-             jk++;
+                                         /* 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 */
-           printf("\n");
+                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           fprintf(ficlog,"\n");
+                                         vlv= nbcode[Tvaraff[k]][lv];
-           fprintf(ficres,"\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 *\/ */
-       }
+                                         /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/
-     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+                                         if(k==cptcoveff){
-     if(mle>=1)
+                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
++(cpt-1),  cpt );
-     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+                                         }else{
-     /* # 121 Var(a12)\n\ */
+                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                                                 kl++;
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                                         }
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+                                 } /* end covariate */
-     /* # 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\ */
+                         fprintf(ficgp,"\nset out \n");
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     } /* k1 */
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   } /* cpt */
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++) {
-     /* Just to have a covariance matrix which will be more understandable
-        even is we still don't want to manage dictionary of variables
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     */
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     for(itimes=1;itimes<=2;itimes++){
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-       jj=0;
+                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       for(i=1; i <=nlstate; i++){
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         for(j=1; j <=nlstate+ndeath; j++){
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           if(j==i) continue;
+                                 vlv= nbcode[Tvaraff[k]][lv];
-           for(k=1; k<=ncovmodel;k++){
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-             jj++;
+       }
-             ca[0]= k+'a'-1;ca[1]='\0';
+       fprintf(ficgp,"\n#\n");
-             if(itimes==1){
+                         if(invalidvarcomb[k1]){
-               if(mle>=1)
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                 printf("#%1d%1d%d",i,j,k);
+                                                 continue;
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+                         }
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
-             }else{
+                         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-               if(mle>=1)
+                         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-                 printf("%1d%1d%d",i,j,k);
+                                 if(vpopbased==0)
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+                                         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+                                 else
-             }
+                                         fprintf(ficgp,"\nreplot ");
-             ll=0;
+                                 for (i=1; i<= nlstate+1 ; i ++) {
-             for(li=1;li <=nlstate; li++){
+                                         k=2*i;
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+                                         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);
-                 if(lj==li) continue;
+                                         for (j=1; j<= nlstate+1 ; j ++) {
-                 for(lk=1;lk<=ncovmodel;lk++){
+                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");
-                   ll++;
+                                                 else fprintf(ficgp," %%*lf (%%*lf)");
-                   if(ll<=jj){
+                                         }
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+                                         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-                     if(ll<jj){
+                                         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-                       if(itimes==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);
-                         if(mle>=1)
+                                         for (j=1; j<= nlstate+1 ; j ++) {
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                                 else fprintf(ficgp," %%*lf (%%*lf)");
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                         }
-                       }else{
+                                         fprintf(ficgp,"\" t\"\" w l lt 0,");
-                         if(mle>=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);
-                           printf(" %.5e",matcov[jj][ll]);
+                                         for (j=1; j<= nlstate+1 ; j ++) {
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                                                 else fprintf(ficgp," %%*lf (%%*lf)");
-                       }
+                                         }
-                     }else{
+                                         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-                       if(itimes==1){
+                                         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-                         if(mle>=1)
+                                 } /* state */
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         } /* vpopbased */
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+   } /* k1 */
-                       }else{
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+   /*3eme*/
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   for (k1=1; k1<= m ; k1 ++) {
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-                     }
+       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 */
-                 } /* end lk */
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-               } /* end lj */
+                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-             } /* end li */
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-             if(mle>=1)
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-               printf("\n");
+                                 vlv= nbcode[Tvaraff[k]][lv];
-             fprintf(ficlog,"\n");
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-             fprintf(ficres,"\n");
+       }
-             numlinepar++;
+       fprintf(ficgp,"\n#\n");
-           } /* end k*/
+                         if(invalidvarcomb[k1]){
-         } /*end j */
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       } /* end i */
+                                                 continue;
-     } /* end itimes */
+                         }
-     fflush(ficlog);
+       /*       k=2+nlstate*(2*cpt-2); */
-     fflush(ficres);
+       k=2+(nlstate+1)*(cpt-1);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficgp,"set ter svg size 640, 480\n\
-       ungetc(c,ficpar);
+ 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);
-       fgets(line, MAXLINE, ficpar);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-       puts(line);
+                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-       fputs(line,ficparo);
+                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     }
+                                 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     ungetc(c,ficpar);
+                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+       */
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+       for (i=1; i< nlstate ; i ++) {
-     if (fage <= 2) {
+                                 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);
-       bage = ageminpar;
+                                 /*      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);*/
-       fage = agemaxpar;
-     }
+       }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     }
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   }
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+         /* 4eme */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   /* Survival functions (period) from state i in state j by initial state i */
-       ungetc(c,ficpar);
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-       fputs(line,ficparo);
+       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 */
-     ungetc(c,ficpar);
+                                 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 */
-     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);
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     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);
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     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);
+                                 vlv= nbcode[Tvaraff[k]][lv];
-     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(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     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);
+       }
+       fprintf(ficgp,"\n#\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+                         if(invalidvarcomb[k1]){
-       ungetc(c,ficpar);
+                                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       fgets(line, MAXLINE, ficpar);
+                                                         continue;
-       puts(line);
+                         }
-       fputs(line,ficparo);
-     }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
-     ungetc(c,ficpar);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\n                                                                                                                                                                                     \
+ unset log y\n                                                                                                                                                                                                                                           \
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+       k=3;
+       for (i=1; i<= nlstate ; i ++){
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+                                 if(i==1){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-     fprintf(ficres,"pop_based=%d\n",popbased);
+                                 }else{
+                                         fprintf(ficgp,", '' ");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+                                 }
-       ungetc(c,ficpar);
+                                 l=(nlstate+ndeath)*(i-1)+1;
-       fgets(line, MAXLINE, ficpar);
+                                 fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-       puts(line);
+                                 for (j=2; j<= nlstate+ndeath ; j ++)
-       fputs(line,ficparo);
+                                         fprintf(ficgp,"+$%d",k+l+j-1);
-     }
+                                 fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
-     ungetc(c,ficpar);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
-     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);
+     } /* end cpt state*/
-     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);
+   } /* end covariate */
-     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);
+ /* 5eme */
-     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);
+   /* Survival functions (period) from state i in state j by final state j */
-     /* day and month of proj2 are not used but only year anproj2.*/
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+       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);
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+                                 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 */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+                                 vlv= nbcode[Tvaraff[k]][lv];
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+       }
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+       fprintf(ficgp,"\n#\n");
+                         if(invalidvarcomb[k1]){
-    /*------------ free_vector  -------------*/
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-    /*  chdir(path); */
+                                                 continue;
+                         }
-     free_ivector(wav,1,imx);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+ set ter svg size 640, 480\n                                                                                                                                                                                     \
-     free_lvector(num,1,n);
+ unset log y\n                                                                                                                                                                                                                                           \
-     free_vector(agedc,1,n);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+       k=3;
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-     fclose(ficparo);
+                                 if(j==1)
-     fclose(ficres);
+                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+                                 else
+                                         fprintf(ficgp,", '' ");
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+                                 l=(nlstate+ndeath)*(cpt-1) +j;
+                                 fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-     strcpy(filerespl,"pl");
+                                 /* for (i=2; i<= nlstate+ndeath ; i ++) */
-     strcat(filerespl,fileres);
+                                 /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+                                 fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+       } /* nlstate */
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+       fprintf(ficgp,", '' ");
-     }
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+                                 l=(nlstate+ndeath)*(cpt-1) +j;
-     pstamp(ficrespl);
+                                 if(j < nlstate)
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+                                         fprintf(ficgp,"$%d +",k+l);
-     fprintf(ficrespl,"#Age ");
+                                 else
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+                                         fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-     fprintf(ficrespl,"\n");
+       }
+       fprintf(ficgp,"\nset out\n");
-     prlim=matrix(1,nlstate,1,nlstate);
+     } /* end cpt state*/
+   } /* end covariate */
-     agebase=ageminpar;
-     agelim=agemaxpar;
+ /* 6eme */
-     ftolpl=1.e-10;
+   /* CV preval stable (period) for each covariate */
-     i1=cptcoveff;
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
-     if (cptcovn < 1){i1=1;}
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         k=k+1;
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         fprintf(ficrespl,"\n#******");
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         printf("\n#******");
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         fprintf(ficlog,"\n#******");
+                                 vlv= nbcode[Tvaraff[k]][lv];
-         for(j=1;j<=cptcoveff;j++) {
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficgp,"\n#\n");
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                         if(invalidvarcomb[k1]){
-         }
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         fprintf(ficrespl,"******\n");
+                                                 continue;
-         printf("******\n");
+                         }
-         fprintf(ficlog,"******\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
-         for (age=agebase; age<=agelim; age++){
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+ set ter svg size 640, 480\n\
-           fprintf(ficrespl,"%.0f ",age );
+ unset log y\n\
-           for(j=1;j<=cptcoveff;j++)
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       k=3; /* Offset */
-           for(i=1; i<=nlstate;i++)
+       for (i=1; i<= nlstate ; i ++){
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+                                 if(i==1)
-           fprintf(ficrespl,"\n");
+                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         }
+                                 else
-       }
+                                         fprintf(ficgp,", '' ");
-     }
+                                 l=(nlstate+ndeath)*(i-1)+1;
-     fclose(ficrespl);
+                                 fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+                                 for (j=2; j<= nlstate ; j ++)
-     /*------------- h Pij x at various ages ------------*/
+                                         fprintf(ficgp,"+$%d",k+l+j-1);
+                                 fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+       } /* nlstate */
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       fprintf(ficgp,"\nset out\n");
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     } /* end cpt state*/
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+   } /* end covariate */
-     }
-     printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+ /* 7eme */
+   if(backcast == 1){
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /* CV back preval stable (period) for each covariate */
-     /*if (stepm<=24) stepsize=2;*/
+     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 */
-     agelim=AGESUP;
+                                 fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
-     hstepm=stepsize*YEARM; /* Every year of age */
+                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+                                         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 */
-     /* hstepm=1;   aff par mois*/
+                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     pstamp(ficrespij);
+                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+                                         vlv= nbcode[Tvaraff[k]][lv];
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+                                 }
-         k=k+1;
+                                 fprintf(ficgp,"\n#\n");
-         fprintf(ficrespij,"\n#****** ");
+                                 if(invalidvarcomb[k1]){
-         for(j=1;j<=cptcoveff;j++)
+                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                                                                 continue;
-         fprintf(ficrespij,"******\n");
+                                 }
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+ set ter svg size 640, 480\n                                                                                                                                                                                     \
+ unset log y\n                                                                                                                                                                                                                                           \
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+                                 k=3; /* Offset */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                 for (i=1; i<= nlstate ; i ++){
-           oldm=oldms;savm=savms;
+                                         if(i==1)
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+                                         else
-           for(i=1; i<=nlstate;i++)
+                                                 fprintf(ficgp,", '' ");
-             for(j=1; j<=nlstate+ndeath;j++)
+                                         /* l=(nlstate+ndeath)*(i-1)+1; */
-               fprintf(ficrespij," %1d-%1d",i,j);
+                                         l=(nlstate+ndeath)*(cpt-1)+1;
-           fprintf(ficrespij,"\n");
+                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
-           for (h=0; h<=nhstepm; h++){
+                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+                                         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
-             for(i=1; i<=nlstate;i++)
+                                         /* for (j=2; j<= nlstate ; j ++) */
-               for(j=1; j<=nlstate+ndeath;j++)
+                                         /*      fprintf(ficgp,"+$%d",k+l+j-1); */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+                                         /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-             fprintf(ficrespij,"\n");
+                                         fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
-           }
+                                 } /* nlstate */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                 fprintf(ficgp,"\nset out\n");
-           fprintf(ficrespij,"\n");
+       } /* end cpt state*/
-         }
+     } /* end covariate */
-       }
+   } /* End if backcast */
-     }
+         /* 8eme */
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   if(prevfcast==1){
+     /* Projection from cross-sectional to stable (period) for each covariate */
-     fclose(ficrespij);
+     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-     for(i=1;i<=AGESUP;i++)
+                                 fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
-       for(j=1;j<=NCOVMAX;j++)
+                                 for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
-         for(k=1;k<=NCOVMAX;k++)
+                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-           probs[i][j][k]=0.;
+                                         /* 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 */
-     /*---------- Forecasting ------------------*/
+                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+                                         vlv= nbcode[Tvaraff[k]][lv];
-     if(prevfcast==1){
+                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       /*    if(stepm ==1){*/
+                                 }
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+                                 fprintf(ficgp,"\n#\n");
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+                                 if(invalidvarcomb[k1]){
-       /*      }  */
+                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       /*      else{ */
+                                                                 continue;
-       /*        erreur=108; */
+                                 }
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+                                 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   \
-     /*---------- Health expectancies and variances ------------*/
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
-     strcpy(filerest,"t");
+                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-     strcat(filerest,fileres);
+                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+                                         /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+                                         /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+                                         if(i==1){
-     }
+                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+                                         }else{
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+                                                 fprintf(ficgp,",\\\n '' ");
+                                         }
+                                         if(cptcoveff ==0){ /* No covariate */
-     strcpy(filerese,"e");
+                                                 ioffset=2; /* Age is in 2 */
-     strcat(filerese,fileres);
+                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+                                                 /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+                                                 /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
-     }
+                                                 fprintf(ficgp," u %d:(", ioffset);
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+                                                 if(i==nlstate+1)
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+                                                         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 );
-     strcpy(fileresstde,"stde");
+                                                 else
-     strcat(fileresstde,fileres);
+                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+                                         }else{ /* more than 2 covariates */
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+                                                 if(cptcoveff ==1){
-     }
+                                                         ioffset=4; /* Age is in 4 */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+                                                 }else{
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+                                                         ioffset=6; /* Age is in 6 */
+                                                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-     strcpy(filerescve,"cve");
+                                                 /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-     strcat(filerescve,fileres);
+                                                 }
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+                                                 fprintf(ficgp," u %d:(",ioffset);
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+                                                 kl=0;
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+                                                 strcpy(gplotcondition,"(");
-     }
+                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+                                                         /* 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 */
-     strcpy(fileresv,"v");
+                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-     strcat(fileresv,fileres);
+                                                         vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+                                                         kl++;
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+                                                         kl++;
-     }
+                                                         if(k <cptcoveff && cptcoveff>1)
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+                                                 }
+                                                 strcpy(gplotcondition+strlen(gplotcondition),")");
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+                                                 /* 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 *\/ */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+                                                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
-     /*  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",\
+                                                 /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+                                                 /* ''  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, \
-     if (mobilav!=0) {
+                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                                                 }else{
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+                                                                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                                                 }
-       }
+                                         } /* end if covariate */
-     }
+                                 } /* nlstate */
+                                 fprintf(ficgp,"\nset out\n");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+                         } /* end cpt state*/
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+                 } /* end covariate */
-         k=k+1;
+         } /* End if prevfcast */
-         fprintf(ficrest,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         /* proba elementaires */
-         fprintf(ficrest,"******\n");
+         fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   for(i=1,jk=1; i <=nlstate; i++){
-         fprintf(ficreseij,"\n#****** ");
+     fprintf(ficgp,"# initial state %d\n",i);
-         fprintf(ficresstdeij,"\n#****** ");
+     for(k=1; k <=(nlstate+ndeath); k++){
-         fprintf(ficrescveij,"\n#****** ");
+       if (k != i) {
-         for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficgp,"#   current state %d\n",k);
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         for(j=1; j <=ncovmodel; j++){
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           jk++;
          }
-         fprintf(ficreseij,"******\n");
+         fprintf(ficgp,"\n");
-         fprintf(ficresstdeij,"******\n");
+       }
-         fprintf(ficrescveij,"******\n");
+     }
+    }
-         fprintf(ficresvij,"\n#****** ");
+   fprintf(ficgp,"##############\n#\n");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   /*goto avoid;*/
-         fprintf(ficresvij,"******\n");
+   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");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-         oldm=oldms;savm=savms;
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+   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");
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-         oldm=oldms;savm=savms;
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
-         if(popbased==1){
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+   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");
-         pstamp(ficrest);
+    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+      fprintf(ficgp,"# ng=%d\n",ng);
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
-         fprintf(ficrest,"\n");
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"#    jk=%d\n",jk);
-         epj=vector(1,nlstate+1);
+        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
-         for(age=bage; age <=fage ;age++){
+        fprintf(ficgp,"\nset ter svg size 640, 480 ");
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+        if (ng==1){
-           if (popbased==1) {
+          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
-             if(mobilav ==0){
+          fprintf(ficgp,"\nunset log y");
-               for(i=1; i<=nlstate;i++)
+        }else if (ng==2){
-                 prlim[i][i]=probs[(int)age][i][k];
+          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
-             }else{ /* mobilav */
+          fprintf(ficgp,"\nset log y");
-               for(i=1; i<=nlstate;i++)
+        }else if (ng==3){
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-             }
+          fprintf(ficgp,"\nset log y");
-           }
+        }else
+          fprintf(ficgp,"\nunset title ");
-           fprintf(ficrest," %4.0f",age);
+        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+        i=1;
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+        for(k2=1; k2<=nlstate; k2++) {
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+          k3=i;
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+          for(k=1; k<=(nlstate+ndeath); k++) {
-             }
+            if (k != k2){
-             epj[nlstate+1] +=epj[j];
+              switch( ng) {
-           }
+              case 1:
+                if(nagesqr==0)
-           for(i=1, vepp=0.;i <=nlstate;i++)
+                  fprintf(ficgp," p%d+p%d*x",i,i+1);
-             for(j=1;j <=nlstate;j++)
+                else /* nagesqr =1 */
-               vepp += vareij[i][j][(int)age];
+                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+                break;
-           for(j=1;j <=nlstate;j++){
+              case 2: /* ng=2 */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+                if(nagesqr==0)
-           }
+                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-           fprintf(ficrest,"\n");
+                else /* nagesqr =1 */
-         }
+                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+                break;
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+              case 3:
-         free_vector(epj,1,nlstate+1);
+                if(nagesqr==0)
-       }
+                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-     }
+                else /* nagesqr =1 */
-     free_vector(weight,1,n);
+                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
-     free_imatrix(Tvard,1,15,1,2);
+                break;
-     free_imatrix(s,1,maxwav+1,1,n);
+              }
-     free_matrix(anint,1,maxwav,1,n);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-     free_matrix(mint,1,maxwav,1,n);
+              for(j=3; j <=ncovmodel-nagesqr; j++) {
-     free_ivector(cod,1,n);
+                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-     free_ivector(tab,1,NCOVMAX);
+                if(ij <=cptcovage) { /* Bug valgrind */
-     fclose(ficreseij);
+                  if((j-2)==Tage[ij]) { /* Bug valgrind */
-     fclose(ficresstdeij);
+                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-     fclose(ficrescveij);
+                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-     fclose(ficresvij);
+                    ij++;
-     fclose(ficrest);
+                  }
-     fclose(ficpar);
+                }
+                else
-     /*------- Variance of period (stable) prevalence------*/
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+              }
-     strcpy(fileresvpl,"vpl");
+            }else{
-     strcat(fileresvpl,fileres);
+              i=i-ncovmodel;
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+                fprintf(ficgp," (1.");
-       exit(0);
+            }
-     }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+            if(ng != 1){
+              fprintf(ficgp,")/(1");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+              for(k1=1; k1 <=nlstate; k1++){
-         k=k+1;
+                if(nagesqr==0)
-         fprintf(ficresvpl,"\n#****** ");
+                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-         for(j=1;j<=cptcoveff;j++)
+                else /* nagesqr =1 */
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                  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);
-         fprintf(ficresvpl,"******\n");
+                ij=1;
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+                for(j=3; j <=ncovmodel-nagesqr; j++){
-         oldm=oldms;savm=savms;
+                  if(ij <=cptcovage) { /* Bug valgrind */
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+                    if((j-2)==Tage[ij]) { /* Bug valgrind */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+                      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++;
+                    }
-     fclose(ficresvpl);
+                  }
+                  else
-     /*---------- End : free ----------------*/
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                }
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                fprintf(ficgp,")");
+              }
-   }  /* mle==-3 arrives here for freeing */
+              fprintf(ficgp,")");
-   free_matrix(prlim,1,nlstate,1,nlstate);
+              if(ng ==2)
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+                fprintf(ficgp," t \"p%d%d\" ", k2,k);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+              else /* ng= 3 */
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+                fprintf(ficgp," t \"i%d%d\" ", k2,k);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+            }else{ /* end ng <> 1 */
-     free_matrix(covar,0,NCOVMAX,1,n);
+              if( k !=k2) /* logit p11 is hard to draw */
-     free_matrix(matcov,1,npar,1,npar);
+                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
-     /*free_vector(delti,1,npar);*/
+            }
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
-     free_matrix(agev,1,maxwav,1,imx);
+              fprintf(ficgp,",");
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
+              fprintf(ficgp,",");
-     free_ivector(ncodemax,1,8);
+            i=i+ncovmodel;
-     free_ivector(Tvar,1,15);
+          } /* end k */
-     free_ivector(Tprod,1,15);
+        } /* end k2 */
-     free_ivector(Tvaraff,1,15);
+        fprintf(ficgp,"\n set out\n");
-     free_ivector(Tage,1,15);
+      } /* end jk */
-     free_ivector(Tcode,1,100);
+    } /* end ng */
+  /* avoid: */
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+    fflush(ficgp);
-     free_imatrix(codtab,1,100,1,10);
+ }  /* end gnuplot */
-   fflush(fichtm);
-   fflush(ficgp);
+ /*************** Moving average **************/
+ /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
-   if((nberr >0) || (nbwarn>0)){
+ int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   int i, cpt, cptcod;
-   }else{
+   int modcovmax =1;
-     printf("End of Imach\n");
+   int mobilavrange, mob;
-     fprintf(ficlog,"End of Imach\n");
+   int iage=0;
-   }
-   printf("See log file on %s\n",filelog);
+   double sum=0.;
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   double age;
-   (void) gettimeofday(&end_time,&tzp);
+   double *sumnewp, *sumnewm;
-   tm = *localtime(&end_time.tv_sec);
+   double *agemingood, *agemaxgood; /* Currently identical for all covariates */
-   tmg = *gmtime(&end_time.tv_sec);
-   strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+         /*                 a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   sumnewp = vector(1,ncovcombmax);
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   sumnewm = vector(1,ncovcombmax);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   agemingood = vector(1,ncovcombmax);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   agemaxgood = vector(1,ncovcombmax);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+                 sumnewm[cptcod]=0.;
-   fclose(fichtm);
+                 sumnewp[cptcod]=0.;
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+                 agemingood[cptcod]=0;
-   fclose(fichtmcov);
+                 agemaxgood[cptcod]=0;
-   fclose(ficgp);
+         }
-   fclose(ficlog);
+   if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-   /*------ End -----------*/
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+     if(mobilav==1) mobilavrange=5; /* default */
-    printf("Before Current directory %s!\n",pathcd);
+     else mobilavrange=mobilav;
-    if(chdir(pathcd) != 0)
+     for (age=bage; age<=fage; age++)
-     printf("Can't move to directory %s!\n",path);
+       for (i=1; i<=nlstate;i++)
-   if(getcwd(pathcd,MAXLINE) > 0)
+                                 for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
-     printf("Current directory %s!\n",pathcd);
+                                         mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     /* We keep the original values on the extreme ages bage, fage and for
-   sprintf(plotcmd,"gnuplot");
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
- #ifndef UNIX
+        we use a 5 terms etc. until the borders are no more concerned.
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+     */
- #endif
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-   if(!stat(plotcmd,&info)){
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+                                 for (i=1; i<=nlstate;i++){
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+                                         for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+                                                 mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-     }else
+                                                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
-       strcpy(pplotcmd,plotcmd);
+                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
- #ifdef UNIX
+                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+                                                 }
-     if(!stat(plotcmd,&info)){
+                                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+                                         }
-     }else
+                                 }
-       strcpy(pplotcmd,plotcmd);
+       }/* end age */
- #endif
+     }/* end mob */
    }else
-     strcpy(pplotcmd,plotcmd);
+     return -1;
+   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     agemingood[cptcod]=fage-(mob-1)/2;
+     for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
-   if((outcmd=system(plotcmd)) != 0){
+       sumnewm[cptcod]=0.;
-     printf("\n Problem with gnuplot\n");
+       for (i=1; i<=nlstate;i++){
-   }
+         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-   printf(" Wait...");
+       }
-   while (z[0] != 'q') {
+       if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-     /* chdir(path); */
+                                 agemingood[cptcod]=age;
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+       }else{ /* bad */
-     scanf("%s",z);
+                                 for (i=1; i<=nlstate;i++){
- /*     if (z[0] == 'c') system("./imach"); */
+                                         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
-     if (z[0] == 'e') {
+                                 } /* i */
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       } /* end bad */
-       system(optionfilehtm);
+     }/* age */
-     }
+     sum=0.;
-     else if (z[0] == 'g') system(plotcmd);
+     for (i=1; i<=nlstate;i++){
-     else if (z[0] == 'q') exit(0);
+       sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
-   }
+     }
-   end:
+     if(fabs(sum - 1.) > 1.e-3) { /* bad */
-   while (z[0] != 'q') {
+       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);
-     printf("\nType  q for exiting: ");
+       /* for (i=1; i<=nlstate;i++){ */
-     scanf("%s",z);
+       /*   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=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(cptcov=1, k=0;cptcov<=i1;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       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][cptcod];
+                                                                 else {
+                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                                                                 }
+                                                                 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 cptcod */
+   } /* end  cptcov */
+   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 dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double 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;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[MAXLINE], strb[MAXLINE];
+   char *stratrunc;
+   int lstra;
+   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);
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           return 1;
+         }
+       }
+       s[j][i]=lval;
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+       }
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
+         month=99;
+         year=9999;
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         return 1;
+       }
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
+     } /* ENd Waves */
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
+     errno=0;
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fflush(ficlog);
+       return 1;
+     }
+     weight[i]=dval;
+     strcpy(line,stra);
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           return 1;
+         }
+       }
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+         return 1;
+       }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
+     }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
+   return (0);
+   /* endread: */
+     printf("Exiting readdata: ");
+     fclose(fic);
+     return (1);
+ }
+ void removespace(char *str) {
+   char *p1 = str, *p2 = str;
+   do
+     while (*p2 == ' ')
+       p2++;
+   while (*p1++ == *p2++);
+ }
+ int decodemodel ( char model[], int lastobs) /**< This routine decode 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;
+   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 =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=> 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]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+        *  Tage[++cptcovage]=k
+        *       if products, new covar are created after ncovcol with k1
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+        *  <          ncovcol=8                >
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tprod[1]@2={                         6, 5}
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+        *How to reorganize?
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
+        * Struct []
+        */
+       /* 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 */
+         Tvar[k]=0;
+       cptcovage=0;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*scanf("%d",i);*/
+         if (strchr(strb,'*')) {  /**< Model includes a product 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 */
+             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);
+             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+k1; /* 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+V3*V2
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+             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  */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             k2=k2+2;
+             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+             for (i=1; i<=lastobs;i++){
+               /* Computes the new covariate which is a product of
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+             }
+           } /* End age is not in the model */
+         } /* End if model includes a product */
+         else { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates */
+           cptcovn++;
+           Tvar[k]=atoi(strd);
+         }
+         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);*/
+   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("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"Computing 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,cptcoveff);
+   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++) {
+       fprintf(ficrespl," 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(ficrespl,"******\n");
+     printf("******\n");
+     fprintf(ficlog,"******\n");
+                 if(invalidvarcomb[k]){
+                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \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++){
+   /* 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(ficresplb,"#******");
+     printf("#******");
+     fprintf(ficlog,"#******");
+     for(j=1;j<=cptcoveff;j++) {
+       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");
+     /* 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 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 nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+     if (num_filled != 8) {
+       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       printf("but line=%s\n",line);
+     }
+     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, 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 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(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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,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 */
+   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%1d",&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%1d",i1,j1,jk);
+                         }
+       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%1d",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. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
+ /* Main decodemodel */
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   /* free_vector(moisdc,1,n); */
+   /* free_vector(andc,1,n); */
+   /* */
+   wav=ivector(1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   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 nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+                                 if (k != i) {
+                                         printf("%d%d ",i,k);
+                                         fprintf(ficlog,"%d%d ",i,k);
+                                         fprintf(ficres,"%1d%1d ",i,k);
+                                         for(j=1; j <=ncovmodel; j++){
+                                                 printf("%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.*/
+                 /* 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++){
+       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);
+     /*---------- Health 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 Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"CVE_");
+     strcat(filerescve,fileresu);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"V_");
+     strcat(fileresv,fileresu);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
+     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrest,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrest,"******\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 %d, ",k);
+       fprintf(ficlog, " cvevsij %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 %d \n",vpopbased);
+                                 fprintf(ficlog, "varevsij %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 */
+     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);
+     printf("done Health expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
+     fclose(ficpar);
+     /*------- 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#****** ");
+                         for(j=1;j<=cptcoveff;j++)
+                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+                         fprintf(ficresvpl,"******\n");
+                         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+                         oldm=oldms;savm=savms;
+                         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &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);
+     /*---------- 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_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(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(invalidvarcomb,1,ncovcombmax);
+     free_ivector(Tage,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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