Diff for /imach/src/imach.c between versions 1.125 and 1.224

version 1.125, 2006/04/04 15:20:31 version 1.224, 2016/07/01 13:16:01
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.224  2016/07/01 13:16:01  brouard
     Summary: Fixes
   
     Revision 1.223  2016/02/19 09:23:35  brouard
     Summary: temporary
   
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
     Revision 1.221  2016/02/15 23:35:36  brouard
     Summary: minor bug
   
     Revision 1.219  2016/02/15 00:48:12  brouard
     *** empty log message ***
   
     Revision 1.218  2016/02/12 11:29:23  brouard
     Summary: 0.99 Back projections
   
     Revision 1.217  2015/12/23 17:18:31  brouard
     Summary: Experimental backcast
   
     Revision 1.216  2015/12/18 17:32:11  brouard
     Summary: 0.98r4 Warning and status=-2
   
     Version 0.98r4 is now:
      - displaying an error when status is -1, date of interview unknown and date of death known;
      - permitting a status -2 when the vital status is unknown at a known date of right truncation.
     Older changes concerning s=-2, dating from 2005 have been supersed.
   
     Revision 1.215  2015/12/16 08:52:24  brouard
     Summary: 0.98r4 working
   
     Revision 1.214  2015/12/16 06:57:54  brouard
     Summary: temporary not working
   
     Revision 1.213  2015/12/11 18:22:17  brouard
     Summary: 0.98r4
   
     Revision 1.212  2015/11/21 12:47:24  brouard
     Summary: minor typo
   
     Revision 1.211  2015/11/21 12:41:11  brouard
     Summary: 0.98r3 with some graph of projected cross-sectional
   
     Author: Nicolas Brouard
   
     Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
     Revision 1.209  2015/11/17 22:12:03  brouard
     Summary: Adding ftolpl parameter
     Author: N Brouard
   
     We had difficulties to get smoothed confidence intervals. It was due
     to the period prevalence which wasn't computed accurately. The inner
     parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
     computation are long.
   
     Revision 1.208  2015/11/17 14:31:57  brouard
     Summary: temporary
   
     Revision 1.207  2015/10/27 17:36:57  brouard
     *** empty log message ***
   
     Revision 1.206  2015/10/24 07:14:11  brouard
     *** empty log message ***
   
     Revision 1.205  2015/10/23 15:50:53  brouard
     Summary: 0.98r3 some clarification for graphs on likelihood contributions
   
     Revision 1.204  2015/10/01 16:20:26  brouard
     Summary: Some new graphs of contribution to likelihood
   
     Revision 1.203  2015/09/30 17:45:14  brouard
     Summary: looking at better estimation of the hessian
   
     Also a better criteria for convergence to the period prevalence And
     therefore adding the number of years needed to converge. (The
     prevalence in any alive state shold sum to one
   
     Revision 1.202  2015/09/22 19:45:16  brouard
     Summary: Adding some overall graph on contribution to likelihood. Might change
   
     Revision 1.201  2015/09/15 17:34:58  brouard
     Summary: 0.98r0
   
     - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
   
     Revision 1.200  2015/09/09 16:53:55  brouard
     Summary: Big bug thanks to Flavia
   
     Even model=1+age+V2. did not work anymore
   
     Revision 1.199  2015/09/07 14:09:23  brouard
     Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   
     Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
   
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
     Revision 1.194  2015/08/18 13:32:00  brouard
     Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
     Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
     Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   
     Revision 1.190  2015/05/05 08:51:13  brouard
     Summary: Adding digits in output parameters (7 digits instead of 6)
   
     Fix 1+age+.
   
     Revision 1.189  2015/04/30 14:45:16  brouard
     Summary: 0.98q2
   
     Revision 1.188  2015/04/30 08:27:53  brouard
     *** empty log message ***
   
     Revision 1.187  2015/04/29 09:11:15  brouard
     *** empty log message ***
   
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
     Revision 1.183  2015/03/10 20:34:32  brouard
     Summary: 0.98q0, trying with directest, mnbrak fixed
   
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
     Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
     Author: Nicolas Brouard
   
     Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
     Author:
   
     Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
     Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   
     Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
     Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
   
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
     Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
   
     Testing on Linux 64
   
     Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
   
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
   
     Revision 1.1  2014/09/16 11:06:58  brouard
     Summary: With some code (wrong) for nlopt
   
     Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
   
     Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
   
     Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
     Author: Brouard
   
     Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   
     Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
     Author: Brouard
   
     In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
   
     Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
   
     Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
     Author: Brouard
   
     Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
   
     Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
   
     Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
     Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
   
     Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
   
     Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
   
     Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
     Author: Brouard
   
     Just a new packaging for OS/X version 0.98nS
   
     Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
   
     Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
     Author: Brouard
   
     Merge, before building revised version.
   
     Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
     Author: Nicolas Brouard
   
     Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
     No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
     the source code.
   
     Revision 1.143  2014/01/26 09:45:38  brouard
     Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
     Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
     Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
     Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
   
     Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
     Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
   
     Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
   
     Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
     Some cleaning of code and comments added.
   
     Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
   
     Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
   
     Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
     Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
     Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
     Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
   
     Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
     computation.
     In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
     Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     Version 0.98h
   
   Revision 1.125  2006/04/04 15:20:31  lievre    Revision 1.125  2006/04/04 15:20:31  lievre
   Errors in calculation of health expectancies. Age was not initialized.    Errors in calculation of health expectancies. Age was not initialized.
   Forecasting file added.    Forecasting file added.
   
   Revision 1.124  2006/03/22 17:13:53  lievre    Revision 1.124  2006/03/22 17:13:53  lievre
   Parameters are printed with %lf instead of %f (more numbers after the comma).    Parameters are printed with %lf instead of %f (more numbers after the comma).
   The log-likelihood is printed in the log file    The log-likelihood is printed in the log file
   
   Revision 1.123  2006/03/20 10:52:43  brouard    Revision 1.123  2006/03/20 10:52:43  brouard
   * imach.c (Module): <title> changed, corresponds to .htm file    * imach.c (Module): <title> changed, corresponds to .htm file
   name. <head> headers where missing.    name. <head> headers where missing.
   
   * imach.c (Module): Weights can have a decimal point as for    * imach.c (Module): Weights can have a decimal point as for
   English (a comma might work with a correct LC_NUMERIC environment,    English (a comma might work with a correct LC_NUMERIC environment,
   otherwise the weight is truncated).    otherwise the weight is truncated).
   Modification of warning when the covariates values are not 0 or    Modification of warning when the covariates values are not 0 or
   1.    1.
   Version 0.98g    Version 0.98g
   
   Revision 1.122  2006/03/20 09:45:41  brouard    Revision 1.122  2006/03/20 09:45:41  brouard
   (Module): Weights can have a decimal point as for    (Module): Weights can have a decimal point as for
   English (a comma might work with a correct LC_NUMERIC environment,    English (a comma might work with a correct LC_NUMERIC environment,
   otherwise the weight is truncated).    otherwise the weight is truncated).
   Modification of warning when the covariates values are not 0 or    Modification of warning when the covariates values are not 0 or
   1.    1.
   Version 0.98g    Version 0.98g
   
   Revision 1.121  2006/03/16 17:45:01  lievre    Revision 1.121  2006/03/16 17:45:01  lievre
   * imach.c (Module): Comments concerning covariates added    * imach.c (Module): Comments concerning covariates added
   
   * imach.c (Module): refinements in the computation of lli if    * imach.c (Module): refinements in the computation of lli if
   status=-2 in order to have more reliable computation if stepm is    status=-2 in order to have more reliable computation if stepm is
   not 1 month. Version 0.98f    not 1 month. Version 0.98f
   
   Revision 1.120  2006/03/16 15:10:38  lievre    Revision 1.120  2006/03/16 15:10:38  lievre
   (Module): refinements in the computation of lli if    (Module): refinements in the computation of lli if
   status=-2 in order to have more reliable computation if stepm is    status=-2 in order to have more reliable computation if stepm is
   not 1 month. Version 0.98f    not 1 month. Version 0.98f
   
   Revision 1.119  2006/03/15 17:42:26  brouard    Revision 1.119  2006/03/15 17:42:26  brouard
   (Module): Bug if status = -2, the loglikelihood was    (Module): Bug if status = -2, the loglikelihood was
   computed as likelihood omitting the logarithm. Version O.98e    computed as likelihood omitting the logarithm. Version O.98e
   
   Revision 1.118  2006/03/14 18:20:07  brouard    Revision 1.118  2006/03/14 18:20:07  brouard
   (Module): varevsij Comments added explaining the second    (Module): varevsij Comments added explaining the second
   table of variances if popbased=1 .    table of variances if popbased=1 .
   (Module): Covariances of eij, ekl added, graphs fixed, new html link.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   (Module): Function pstamp added    (Module): Function pstamp added
   (Module): Version 0.98d    (Module): Version 0.98d
   
   Revision 1.117  2006/03/14 17:16:22  brouard    Revision 1.117  2006/03/14 17:16:22  brouard
   (Module): varevsij Comments added explaining the second    (Module): varevsij Comments added explaining the second
   table of variances if popbased=1 .    table of variances if popbased=1 .
   (Module): Covariances of eij, ekl added, graphs fixed, new html link.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   (Module): Function pstamp added    (Module): Function pstamp added
   (Module): Version 0.98d    (Module): Version 0.98d
   
   Revision 1.116  2006/03/06 10:29:27  brouard    Revision 1.116  2006/03/06 10:29:27  brouard
   (Module): Variance-covariance wrong links and    (Module): Variance-covariance wrong links and
   varian-covariance of ej. is needed (Saito).    varian-covariance of ej. is needed (Saito).
   
   Revision 1.115  2006/02/27 12:17:45  brouard    Revision 1.115  2006/02/27 12:17:45  brouard
   (Module): One freematrix added in mlikeli! 0.98c    (Module): One freematrix added in mlikeli! 0.98c
   
   Revision 1.114  2006/02/26 12:57:58  brouard    Revision 1.114  2006/02/26 12:57:58  brouard
   (Module): Some improvements in processing parameter    (Module): Some improvements in processing parameter
   filename with strsep.    filename with strsep.
   
   Revision 1.113  2006/02/24 14:20:24  brouard    Revision 1.113  2006/02/24 14:20:24  brouard
   (Module): Memory leaks checks with valgrind and:    (Module): Memory leaks checks with valgrind and:
   datafile was not closed, some imatrix were not freed and on matrix    datafile was not closed, some imatrix were not freed and on matrix
   allocation too.    allocation too.
   
   Revision 1.112  2006/01/30 09:55:26  brouard    Revision 1.112  2006/01/30 09:55:26  brouard
   (Module): Back to gnuplot.exe instead of wgnuplot.exe    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
   Revision 1.111  2006/01/25 20:38:18  brouard    Revision 1.111  2006/01/25 20:38:18  brouard
   (Module): Lots of cleaning and bugs added (Gompertz)    (Module): Lots of cleaning and bugs added (Gompertz)
   (Module): Comments can be added in data file. Missing date values    (Module): Comments can be added in data file. Missing date values
   can be a simple dot '.'.    can be a simple dot '.'.
   
   Revision 1.110  2006/01/25 00:51:50  brouard    Revision 1.110  2006/01/25 00:51:50  brouard
   (Module): Lots of cleaning and bugs added (Gompertz)    (Module): Lots of cleaning and bugs added (Gompertz)
   
   Revision 1.109  2006/01/24 19:37:15  brouard    Revision 1.109  2006/01/24 19:37:15  brouard
   (Module): Comments (lines starting with a #) are allowed in data.    (Module): Comments (lines starting with a #) are allowed in data.
   
   Revision 1.108  2006/01/19 18:05:42  lievre    Revision 1.108  2006/01/19 18:05:42  lievre
   Gnuplot problem appeared...    Gnuplot problem appeared...
   To be fixed    To be fixed
   
   Revision 1.107  2006/01/19 16:20:37  brouard    Revision 1.107  2006/01/19 16:20:37  brouard
   Test existence of gnuplot in imach path    Test existence of gnuplot in imach path
   
   Revision 1.106  2006/01/19 13:24:36  brouard    Revision 1.106  2006/01/19 13:24:36  brouard
   Some cleaning and links added in html output    Some cleaning and links added in html output
   
   Revision 1.105  2006/01/05 20:23:19  lievre    Revision 1.105  2006/01/05 20:23:19  lievre
   *** empty log message ***    *** empty log message ***
   
   Revision 1.104  2005/09/30 16:11:43  lievre    Revision 1.104  2005/09/30 16:11:43  lievre
   (Module): sump fixed, loop imx fixed, and simplifications.    (Module): sump fixed, loop imx fixed, and simplifications.
   (Module): If the status is missing at the last wave but we know    (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    that the person is alive, then we can code his/her status as -2
   (instead of missing=-1 in earlier versions) and his/her    (instead of missing=-1 in earlier versions) and his/her
   contributions to the likelihood is 1 - Prob of dying from last    contributions to the likelihood is 1 - Prob of dying from last
   health status (= 1-p13= p11+p12 in the easiest case of somebody in    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   the healthy state at last known wave). Version is 0.98    the healthy state at last known wave). Version is 0.98
   
   Revision 1.103  2005/09/30 15:54:49  lievre    Revision 1.103  2005/09/30 15:54:49  lievre
   (Module): sump fixed, loop imx fixed, and simplifications.    (Module): sump fixed, loop imx fixed, and simplifications.
   
   Revision 1.102  2004/09/15 17:31:30  brouard    Revision 1.102  2004/09/15 17:31:30  brouard
   Add the possibility to read data file including tab characters.    Add the possibility to read data file including tab characters.
   
   Revision 1.101  2004/09/15 10:38:38  brouard    Revision 1.101  2004/09/15 10:38:38  brouard
   Fix on curr_time    Fix on curr_time
   
   Revision 1.100  2004/07/12 18:29:06  brouard    Revision 1.100  2004/07/12 18:29:06  brouard
   Add version for Mac OS X. Just define UNIX in Makefile    Add version for Mac OS X. Just define UNIX in Makefile
   
   Revision 1.99  2004/06/05 08:57:40  brouard    Revision 1.99  2004/06/05 08:57:40  brouard
   *** empty log message ***    *** empty log message ***
   
   Revision 1.98  2004/05/16 15:05:56  brouard    Revision 1.98  2004/05/16 15:05:56  brouard
   New version 0.97 . First attempt to estimate force of mortality    New version 0.97 . First attempt to estimate force of mortality
   directly from the data i.e. without the need of knowing the health    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 .    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    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    other analysis, in order to test if the mortality estimated from the
   cross-longitudinal survey is different from the mortality estimated    cross-longitudinal survey is different from the mortality estimated
   from other sources like vital statistic data.    from other sources like vital statistic data.
   
   The same imach parameter file can be used but the option for mle should be -3.    The same imach parameter file can be used but the option for mle should be -3.
   
   Agnès, who wrote this part of the code, tried to keep most of the    Agnès, who wrote this part of the code, tried to keep most of the
   former routines in order to include the new code within the former code.    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 output is very simple: only an estimate of the intercept and of
   the slope with 95% confident intervals.    the slope with 95% confident intervals.
   
   Current limitations:    Current limitations:
   A) Even if you enter covariates, i.e. with the    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.    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.    B) There is no computation of Life Expectancy nor Life Table.
   
   Revision 1.97  2004/02/20 13:25:42  lievre    Revision 1.97  2004/02/20 13:25:42  lievre
   Version 0.96d. Population forecasting command line is (temporarily)    Version 0.96d. Population forecasting command line is (temporarily)
   suppressed.    suppressed.
   
   Revision 1.96  2003/07/15 15:38:55  brouard    Revision 1.96  2003/07/15 15:38:55  brouard
   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   rewritten within the same printf. Workaround: many printfs.    rewritten within the same printf. Workaround: many printfs.
   
   Revision 1.95  2003/07/08 07:54:34  brouard    Revision 1.95  2003/07/08 07:54:34  brouard
   * imach.c (Repository):    * imach.c (Repository):
   (Repository): Using imachwizard code to output a more meaningful covariance    (Repository): Using imachwizard code to output a more meaningful covariance
   matrix (cov(a12,c31) instead of numbers.    matrix (cov(a12,c31) instead of numbers.
   
   Revision 1.94  2003/06/27 13:00:02  brouard    Revision 1.94  2003/06/27 13:00:02  brouard
   Just cleaning    Just cleaning
   
   Revision 1.93  2003/06/25 16:33:55  brouard    Revision 1.93  2003/06/25 16:33:55  brouard
   (Module): On windows (cygwin) function asctime_r doesn't    (Module): On windows (cygwin) function asctime_r doesn't
   exist so I changed back to asctime which exists.    exist so I changed back to asctime which exists.
   (Module): Version 0.96b    (Module): Version 0.96b
   
   Revision 1.92  2003/06/25 16:30:45  brouard    Revision 1.92  2003/06/25 16:30:45  brouard
   (Module): On windows (cygwin) function asctime_r doesn't    (Module): On windows (cygwin) function asctime_r doesn't
   exist so I changed back to asctime which exists.    exist so I changed back to asctime which exists.
   
   Revision 1.91  2003/06/25 15:30:29  brouard    Revision 1.91  2003/06/25 15:30:29  brouard
   * imach.c (Repository): Duplicated warning errors corrected.    * imach.c (Repository): Duplicated warning errors corrected.
   (Repository): Elapsed time after each iteration is now output. It    (Repository): Elapsed time after each iteration is now output. It
   helps to forecast when convergence will be reached. Elapsed time    helps to forecast when convergence will be reached. Elapsed time
   is stamped in powell.  We created a new html file for the graphs    is stamped in powell.  We created a new html file for the graphs
   concerning matrix of covariance. It has extension -cov.htm.    concerning matrix of covariance. It has extension -cov.htm.
   
   Revision 1.90  2003/06/24 12:34:15  brouard    Revision 1.90  2003/06/24 12:34:15  brouard
   (Module): Some bugs corrected for windows. Also, when    (Module): Some bugs corrected for windows. Also, when
   mle=-1 a template is output in file "or"mypar.txt with the design    mle=-1 a template is output in file "or"mypar.txt with the design
   of the covariance matrix to be input.    of the covariance matrix to be input.
   
   Revision 1.89  2003/06/24 12:30:52  brouard    Revision 1.89  2003/06/24 12:30:52  brouard
   (Module): Some bugs corrected for windows. Also, when    (Module): Some bugs corrected for windows. Also, when
   mle=-1 a template is output in file "or"mypar.txt with the design    mle=-1 a template is output in file "or"mypar.txt with the design
   of the covariance matrix to be input.    of the covariance matrix to be input.
   
   Revision 1.88  2003/06/23 17:54:56  brouard    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.    * 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    Revision 1.87  2003/06/18 12:26:01  brouard
   Version 0.96    Version 0.96
   
   Revision 1.86  2003/06/17 20:04:08  brouard    Revision 1.86  2003/06/17 20:04:08  brouard
   (Module): Change position of html and gnuplot routines and added    (Module): Change position of html and gnuplot routines and added
   routine fileappend.    routine fileappend.
   
   Revision 1.85  2003/06/17 13:12:43  brouard    Revision 1.85  2003/06/17 13:12:43  brouard
   * imach.c (Repository): Check when date of death was earlier that    * imach.c (Repository): Check when date of death was earlier that
   current date of interview. It may happen when the death was just    current date of interview. It may happen when the death was just
   prior to the death. In this case, dh was negative and likelihood    prior to the death. In this case, dh was negative and likelihood
   was wrong (infinity). We still send an "Error" but patch by    was wrong (infinity). We still send an "Error" but patch by
   assuming that the date of death was just one stepm after the    assuming that the date of death was just one stepm after the
   interview.    interview.
   (Repository): Because some people have very long ID (first column)    (Repository): Because some people have very long ID (first column)
   we changed int to long in num[] and we added a new lvector for    we changed int to long in num[] and we added a new lvector for
   memory allocation. But we also truncated to 8 characters (left    memory allocation. But we also truncated to 8 characters (left
   truncation)    truncation)
   (Repository): No more line truncation errors.    (Repository): No more line truncation errors.
   
   Revision 1.84  2003/06/13 21:44:43  brouard    Revision 1.84  2003/06/13 21:44:43  brouard
   * imach.c (Repository): Replace "freqsummary" at a correct    * imach.c (Repository): Replace "freqsummary" at a correct
   place. It differs from routine "prevalence" which may be called    place. It differs from routine "prevalence" which may be called
   many times. Probs is memory consuming and must be used with    many times. Probs is memory consuming and must be used with
   parcimony.    parcimony.
   Version 0.95a3 (should output exactly the same maximization than 0.8a2)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
   Revision 1.83  2003/06/10 13:39:11  lievre    Revision 1.83  2003/06/10 13:39:11  lievre
   *** empty log message ***    *** empty log message ***
   
   Revision 1.82  2003/06/05 15:57:20  brouard    Revision 1.82  2003/06/05 15:57:20  brouard
   Add log in  imach.c and  fullversion number is now printed.    Add log in  imach.c and  fullversion number is now printed.
   
 */  */
 /*  /*
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    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    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    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    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    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    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    '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    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    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    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month, quarter,    states. This elementary transition (by month, quarter,
   semester or year) is modelled as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the period (stable) prevalence.    of the life expectancies. It also computes the period (stable) prevalence.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  Back prevalence and projections:
            Institut national d'études démographiques, 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                                                                           1,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
          1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 #include <limits.h>         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 #include <sys/types.h>  
 #include <sys/stat.h>         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 #include <errno.h>         1  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 POWELLNOF3INFF1TEST /* 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  #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[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
 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 ncoveff=0; /* Total number of effective covariates in the model */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int nqveff=0; /**< nqveff number of effective quantitative variables */
   int ntveff=0; /**< ntveff number of effective time varying variables */
 #define GOLD 1.618034  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 #define GLIMIT 100.0  int cptcov=0; /* Working variable */
 #define TINY 1.0e-20  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
   int npar=NPARMAX;
 static double maxarg1,maxarg2;  int nlstate=2; /* Number of live states */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int ndeath=1; /* Number of dead states */
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int popbased=0;
 #define rint(a) floor(a+0.5)  
   int *wav; /* Number of waves for this individuual 0 is possible */
 static double sqrarg;  int maxwav=0; /* Maxim number of waves */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 int agegomp= AGEGOMP;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 int imx;  int mle=1, weightopt=0;
 int stepm=1;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /* Stepm, step in month: minimum step interpolation*/  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
 int estepm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int countcallfunc=0;  /* Count the number of calls to func */
   double jmean=1; /* Mean space between 2 waves */
 int m,nb;  double **matprod2(); /* test */
 long *num;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
 double **pmmij, ***probs;  
 double *ageexmed,*agecens;  /*FILE *fic ; */ /* Used in readdata only */
 double dateintmean=0;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
   FILE *ficlog, *ficrespow;
 double *weight;  int globpr=0; /* Global variable for printing or not */
 int **s; /* Status */  double fretone; /* Only one call to likelihood */
 double *agedc, **covar, idx;  long ipmx=0; /* Number of contributions */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  double sw; /* Sum of weights */
 double *lsurv, *lpop, *tpop;  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  FILE *ficresilk;
 double ftolhess; /* Tolerance for computing hessian */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /**************** split *************************/  FILE *fichtm, *fichtmcov; /* Html File */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)  FILE *ficresstdeij;
      the name of the file (name), its extension only (ext) and its first part of the name (finame)  char fileresstde[FILENAMELENGTH];
   */  FILE *ficrescveij;
   char  *ss;                            /* pointer */  char filerescve[FILENAMELENGTH];
   int   l1, l2;                         /* length counters */  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   l1 = strlen(path );                   /* length of path */  FILE  *ficresvpl;
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char fileresvpl[FILENAMELENGTH];
   ss= strrchr( path, DIRSEPARATOR );            /* find last / */  char title[MAXLINE];
   if ( ss == NULL ) {                   /* no directory, so determine current directory */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
     strcpy( name, path );               /* we got the fullname name because no directory */  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     /*if(strrchr(path, ODIRSEPARATOR )==NULL)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  char command[FILENAMELENGTH];
     /* get current working directory */  int  outcmd=0;
     /*    extern  char* getcwd ( char *buf , int len);*/  
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       return( GLOCK_ERROR_GETCWD );  char fileresu[FILENAMELENGTH]; /* fileres without r in front */
     }  char filelog[FILENAMELENGTH]; /* Log file */
     /* got dirc from getcwd*/  char filerest[FILENAMELENGTH];
     printf(" DIRC = %s \n",dirc);  char fileregp[FILENAMELENGTH];
   } else {                              /* strip direcotry from path */  char popfile[FILENAMELENGTH];
     ss++;                               /* after this, the filename */  
     l2 = strlen( ss );                  /* length of filename */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
     strcpy( name, ss );         /* save file name */  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     strncpy( dirc, path, l1 - l2 );     /* now the directory */  /* struct timezone tzp; */
     dirc[l1-l2] = 0;                    /* add zero */  /* extern int gettimeofday(); */
     printf(" DIRC2 = %s \n",dirc);  struct tm tml, *gmtime(), *localtime();
   }  
   /* We add a separator at the end of dirc if not exists */  extern time_t time();
   l1 = strlen( dirc );                  /* length of directory */  
   if( dirc[l1-1] != DIRSEPARATOR ){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
     dirc[l1] =  DIRSEPARATOR;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     dirc[l1+1] = 0;  struct tm tm;
     printf(" DIRC3 = %s \n",dirc);  
   }  char strcurr[80], strfor[80];
   ss = strrchr( name, '.' );            /* find last / */  
   if (ss >0){  char *endptr;
     ss++;  long lval;
     strcpy(ext,ss);                     /* save extension */  double dval;
     l1= strlen( name);  
     l2= strlen(ss)+1;  #define NR_END 1
     strncpy( finame, name, l1-l2);  #define FREE_ARG char*
     finame[l1-l2]= 0;  #define FTOL 1.0e-10
   }  
   #define NRANSI 
   return( 0 );                          /* we're done */  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
   
 /******************************************/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 void replace_back_to_slash(char *s, char*t)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   int i;  #define GOLD 1.618034 
   int lg=0;  #define GLIMIT 100.0 
   i=0;  #define TINY 1.0e-20 
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  static double maxarg1,maxarg2;
     (s[i] = t[i]);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     if (t[i]== '\\') s[i]='/';  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 int nbocc(char *s, char occ)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
 {  #define mytinydouble 1.0e-16
   int i,j=0;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   int lg=20;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   i=0;  /* static double dsqrarg; */
   lg=strlen(s);  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   for(i=0; i<= lg; i++) {  static double sqrarg;
   if  (s[i] == occ ) j++;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   return j;  int agegomp= AGEGOMP;
 }  
   int imx; 
 void cutv(char *u,char *v, char*t, char occ)  int stepm=1;
 {  /* Stepm, step in month: minimum step interpolation*/
   /* cuts string t into u and v where u ends before first occurence of char 'occ'  
      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')  int estepm;
      gives u="abcedf" and v="ghi2j" */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   int i,lg,j,p=0;  
   i=0;  int m,nb;
   for(j=0; j<=strlen(t)-1; j++) {  long *num;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int firstpass=0, lastpass=4,*cod, *cens;
   }  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                      covariate for which somebody answered excluding 
   lg=strlen(t);                     undefined. Usually 2: 0 and 1. */
   for(j=0; j<p; j++) {  int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
     (u[j] = t[j]);                               covariate for which somebody answered including 
   }                               undefined. Usually 3: -1, 0 and 1. */
      u[p]='\0';  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs; /* Global pointer */
    for(j=0; j<= lg; j++) {  double ***mobaverage, ***mobaverages; /* New global variable */
     if (j>=(p+1))(v[j-p-1] = t[j]);  double *ageexmed,*agecens;
   }  double dateintmean=0;
 }  
   double *weight;
 /********************** nrerror ********************/  int **s; /* Status */
   double *agedc;
 void nrerror(char error_text[])  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 {                    * covar=matrix(0,NCOVMAX,1,n); 
   fprintf(stderr,"ERREUR ...\n");                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   fprintf(stderr,"%s\n",error_text);  double **coqvar; /* Fixed quantitative covariate */
   exit(EXIT_FAILURE);  double ***cotvar; /* Time varying covariate */
 }  double ***cotqvar; /* Time varying quantitative covariate */
 /*********************** vector *******************/  double  idx; 
 double *vector(int nl, int nh)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 {  int *Tage;
   double *v;  int *Ndum; /** Freq of modality (tricode */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
   if (!v) nrerror("allocation failure in vector");  int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
   return v-nl+NR_END;  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 /************************ free vector ******************/  double ftolhess; /**< Tolerance for computing hessian */
 void free_vector(double*v, int nl, int nh)  
 {  /**************** split *************************/
   free((FREE_ARG)(v+nl-NR_END));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 /************************ivector *******************************/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 int *ivector(long nl,long nh)    */ 
 {    char  *ss;                            /* pointer */
   int *v;    int   l1=0, l2=0;                             /* length counters */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    l1 = strlen(path );                   /* length of path */
   return v-nl+NR_END;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
 /******************free ivector **************************/      strcpy( name, path );               /* we got the fullname name because no directory */
 void free_ivector(int *v, long nl, long nh)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   free((FREE_ARG)(v+nl-NR_END));      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
   #ifdef WIN32
 /************************lvector *******************************/      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
 long *lvector(long nl,long nh)  #else
 {          if (getcwd(dirc, FILENAME_MAX) == NULL) {
   long *v;  #endif
   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));        return( GLOCK_ERROR_GETCWD );
   if (!v) nrerror("allocation failure in ivector");      }
   return v-nl+NR_END;      /* got dirc from getcwd*/
 }      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip directory from path */
 /******************free lvector **************************/      ss++;                               /* after this, the filename */
 void free_lvector(long *v, long nl, long nh)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG)(v+nl-NR_END));      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = '\0';                 /* add zero */
 /******************* imatrix *******************************/      printf(" DIRC2 = %s \n",dirc);
 int **imatrix(long nrl, long nrh, long ncl, long nch)    }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    /* We add a separator at the end of dirc if not exists */
 {    l1 = strlen( dirc );                  /* length of directory */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if( dirc[l1-1] != DIRSEPARATOR ){
   int **m;      dirc[l1] =  DIRSEPARATOR;
        dirc[l1+1] = 0; 
   /* allocate pointers to rows */      printf(" DIRC3 = %s \n",dirc);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");    ss = strrchr( name, '.' );            /* find last / */
   m += NR_END;    if (ss >0){
   m -= nrl;      ss++;
        strcpy(ext,ss);                     /* save extension */
        l1= strlen( name);
   /* allocate rows and set pointers to them */      l2= strlen(ss)+1;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      strncpy( finame, name, l1-l2);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      finame[l1-l2]= 0;
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  
      return( 0 );                          /* we're done */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    
   /* return pointer to array of pointers to rows */  
   return m;  /******************************************/
 }  
   void replace_back_to_slash(char *s, char*t)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    int i;
       int **m;    int lg=0;
       long nch,ncl,nrh,nrl;    i=0;
      /* free an int matrix allocated by imatrix() */    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      (s[i] = t[i]);
   free((FREE_ARG) (m+nrl-NR_END));      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  char *trimbb(char *out, char *in)
 {  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    char *s;
   double **m;    s=out;
     while (*in != '\0'){
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   if (!m) nrerror("allocation failure 1 in matrix()");        in++;
   m += NR_END;      }
   m -= nrl;      *out++ = *in++;
     }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    *out='\0';
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return s;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /* char *substrchaine(char *out, char *in, char *chain) */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* { */
   return m;  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])  /*   char *s, *t; */
    */  /*   t=in;s=out; */
 }  /*   while ((*in != *chain) && (*in != '\0')){ */
   /*     *out++ = *in++; */
 /*************************free matrix ************************/  /*   } */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /*   /\* *in matches *chain *\/ */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   free((FREE_ARG)(m+nrl-NR_END));  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
 }  /*   } */
   /*   in--; chain--; */
 /******************* ma3x *******************************/  /*   while ( (*in != '\0')){ */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
 {  /*     *out++ = *in++; */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   double ***m;  /*   } */
   /*   *out='\0'; */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /*   out=s; */
   if (!m) nrerror("allocation failure 1 in matrix()");  /*   return out; */
   m += NR_END;  /* } */
   m -= nrl;  char *substrchaine(char *out, char *in, char *chain)
   {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    /* Substract chain 'chain' from 'in', return and output 'out' */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* in="V1+V1*age+age*age+V2", chain="age*age" */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    char *strloc;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    strcpy (out, in); 
     strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    if(strloc != NULL){ 
   m[nrl][ncl] += NR_END;      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
   m[nrl][ncl] -= nll;      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
   for (j=ncl+1; j<=nch; j++)      /* strcpy (strloc, strloc +strlen(chain));*/
     m[nrl][j]=m[nrl][j-1]+nlay;    }
      printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
   for (i=nrl+1; i<=nrh; i++) {    return out;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  
   }  char *cutl(char *blocc, char *alocc, char *in, char occ)
   return m;  {
   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
            &(m[i][j][k]) <=> *((*(m+i) + j)+k)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   */       gives blocc="abcdef" and alocc="ghi2j".
 }       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
 /*************************free ma3x ************************/    char *s, *t;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    t=in;s=in;
 {    while ((*in != occ) && (*in != '\0')){
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      *alocc++ = *in++;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));    if( *in == occ){
 }      *(alocc)='\0';
       s=++in;
 /*************** function subdirf ***********/    }
 char *subdirf(char fileres[])   
 {    if (s == t) {/* occ not found */
   /* Caution optionfilefiname is hidden */      *(alocc-(in-s))='\0';
   strcpy(tmpout,optionfilefiname);      in=s;
   strcat(tmpout,"/"); /* Add to the right */    }
   strcat(tmpout,fileres);    while ( *in != '\0'){
   return tmpout;      *blocc++ = *in++;
 }    }
   
 /*************** function subdirf2 ***********/    *blocc='\0';
 char *subdirf2(char fileres[], char *preop)    return t;
 {  }
    char *cutv(char *blocc, char *alocc, char *in, char occ)
   /* Caution optionfilefiname is hidden */  {
   strcpy(tmpout,optionfilefiname);    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
   strcat(tmpout,"/");       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   strcat(tmpout,preop);       gives blocc="abcdef2ghi" and alocc="j".
   strcat(tmpout,fileres);       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   return tmpout;    */
 }    char *s, *t;
     t=in;s=in;
 /*************** function subdirf3 ***********/    while (*in != '\0'){
 char *subdirf3(char fileres[], char *preop, char *preop2)      while( *in == occ){
 {        *blocc++ = *in++;
          s=in;
   /* Caution optionfilefiname is hidden */      }
   strcpy(tmpout,optionfilefiname);      *blocc++ = *in++;
   strcat(tmpout,"/");    }
   strcat(tmpout,preop);    if (s == t) /* occ not found */
   strcat(tmpout,preop2);      *(blocc-(in-s))='\0';
   strcat(tmpout,fileres);    else
   return tmpout;      *(blocc-(in-s)-1)='\0';
 }    in=s;
     while ( *in != '\0'){
 /***************** f1dim *************************/      *alocc++ = *in++;
 extern int ncom;    }
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    *alocc='\0';
      return s;
 double f1dim(double x)  }
 {  
   int j;  int nbocc(char *s, char occ)
   double f;  {
   double *xt;    int i,j=0;
      int lg=20;
   xt=vector(1,ncom);    i=0;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    lg=strlen(s);
   f=(*nrfunc)(xt);    for(i=0; i<= lg; i++) {
   free_vector(xt,1,ncom);    if  (s[i] == occ ) j++;
   return f;    }
 }    return j;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /* void cutv(char *u,char *v, char*t, char occ) */
 {  /* { */
   int iter;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   double a,b,d,etemp;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   double fu,fv,fw,fx;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   double ftemp;  /*   int i,lg,j,p=0; */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /*   i=0; */
   double e=0.0;  /*   lg=strlen(t); */
    /*   for(j=0; j<=lg-1; j++) { */
   a=(ax < cx ? ax : cx);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   b=(ax > cx ? ax : cx);  /*   } */
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /*   for(j=0; j<p; j++) { */
   for (iter=1;iter<=ITMAX;iter++) {  /*     (u[j] = t[j]); */
     xm=0.5*(a+b);  /*   } */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /*      u[p]='\0'; */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /*    for(j=0; j<= lg; j++) { */
     fprintf(ficlog,".");fflush(ficlog);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
 #ifdef DEBUG  /*   } */
     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)))) { */  #ifdef _WIN32
 #endif  char * strsep(char **pp, const char *delim)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    char *p, *q;
       return fx;           
     }    if ((p = *pp) == NULL)
     ftemp=fu;      return 0;
     if (fabs(e) > tol1) {    if ((q = strpbrk (p, delim)) != NULL)
       r=(x-w)*(fx-fv);    {
       q=(x-v)*(fx-fw);      *pp = q + 1;
       p=(x-v)*q-(x-w)*r;      *q = '\0';
       q=2.0*(q-r);    }
       if (q > 0.0) p = -p;    else
       q=fabs(q);      *pp = 0;
       etemp=e;    return p;
       e=d;  }
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #endif
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  /********************** nrerror ********************/
         d=p/q;  
         u=x+d;  void nrerror(char error_text[])
         if (u-a < tol2 || b-u < tol2)  {
           d=SIGN(tol1,xm-x);    fprintf(stderr,"ERREUR ...\n");
       }    fprintf(stderr,"%s\n",error_text);
     } else {    exit(EXIT_FAILURE);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  /*********************** vector *******************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  double *vector(int nl, int nh)
     fu=(*f)(u);  {
     if (fu <= fx) {    double *v;
       if (u >= x) a=x; else b=x;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       SHFT(v,w,x,u)    if (!v) nrerror("allocation failure in vector");
         SHFT(fv,fw,fx,fu)    return v-nl+NR_END;
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /************************ free vector ******************/
             v=w;  void free_vector(double*v, int nl, int nh)
             w=u;  {
             fv=fw;    free((FREE_ARG)(v+nl-NR_END));
             fw=fu;  }
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /************************ivector *******************************/
             fv=fu;  int *ivector(long nl,long nh)
           }  {
         }    int *v;
   }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   nrerror("Too many iterations in brent");    if (!v) nrerror("allocation failure in ivector");
   *xmin=x;    return v-nl+NR_END;
   return fx;  }
 }  
   /******************free ivector **************************/
 /****************** mnbrak ***********************/  void free_ivector(int *v, long nl, long nh)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free((FREE_ARG)(v+nl-NR_END));
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /************************lvector *******************************/
   double fu;  long *lvector(long nl,long nh)
    {
   *fa=(*func)(*ax);    long *v;
   *fb=(*func)(*bx);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   if (*fb > *fa) {    if (!v) nrerror("allocation failure in ivector");
     SHFT(dum,*ax,*bx,dum)    return v-nl+NR_END;
       SHFT(dum,*fb,*fa,dum)  }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /******************free lvector **************************/
   *fc=(*func)(*cx);  void free_lvector(long *v, long nl, long nh)
   while (*fb > *fc) {  {
     r=(*bx-*ax)*(*fb-*fc);    free((FREE_ARG)(v+nl-NR_END));
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /******************* imatrix *******************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     if ((*bx-u)*(u-*cx) > 0.0) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       fu=(*func)(u);  { 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       fu=(*func)(u);    int **m; 
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* allocate pointers to rows */ 
           SHFT(*fb,*fc,fu,(*func)(u))    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
           }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m += NR_END; 
       u=ulim;    m -= nrl; 
       fu=(*func)(u);    
     } else {    
       u=(*cx)+GOLD*(*cx-*bx);    /* allocate rows and set pointers to them */ 
       fu=(*func)(u);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     SHFT(*ax,*bx,*cx,u)    m[nrl] += NR_END; 
       SHFT(*fa,*fb,*fc,fu)    m[nrl] -= ncl; 
       }    
 }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
 /*************** linmin ************************/    /* return pointer to array of pointers to rows */ 
     return m; 
 int ncom;  } 
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        int **m;
 {        long nch,ncl,nrh,nrl; 
   double brent(double ax, double bx, double cx,       /* free an int matrix allocated by imatrix() */ 
                double (*f)(double), double tol, double *xmin);  { 
   double f1dim(double x);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG) (m+nrl-NR_END)); 
               double *fc, double (*func)(double));  } 
   int j;  
   double xx,xmin,bx,ax;  /******************* matrix *******************************/
   double fx,fb,fa;  double **matrix(long nrl, long nrh, long ncl, long nch)
    {
   ncom=n;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   pcom=vector(1,n);    double **m;
   xicom=vector(1,n);  
   nrfunc=func;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     pcom[j]=p[j];    m += NR_END;
     xicom[j]=xi[j];    m -= nrl;
   }  
   ax=0.0;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xx=1.0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m[nrl] += NR_END;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    m[nrl] -= ncl;
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return m;
 #endif    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   for (j=1;j<=n;j++) {  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     xi[j] *= xmin;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     p[j] += xi[j];     */
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 char *asc_diff_time(long time_sec, char ascdiff[])    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   long sec_left, days, hours, minutes;  }
   days = (time_sec) / (60*60*24);  
   sec_left = (time_sec) % (60*60*24);  /******************* ma3x *******************************/
   hours = (sec_left) / (60*60) ;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   sec_left = (sec_left) %(60*60);  {
   minutes = (sec_left) /60;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   sec_left = (sec_left) % (60);    double ***m;
   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);    
   return ascdiff;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************** powell ************************/    m -= nrl;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   void linmin(double p[], double xi[], int n, double *fret,    m[nrl] += NR_END;
               double (*func)(double []));    m[nrl] -= ncl;
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double fp,fptt;  
   double *xits;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int niterf, itmp;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   pt=vector(1,n);    m[nrl][ncl] -= nll;
   ptt=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   xit=vector(1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   xits=vector(1,n);    
   *fret=(*func)(p);    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=n;j++) pt[j]=p[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (*iter=1;;++(*iter)) {      for (j=ncl+1; j<=nch; j++) 
     fp=(*fret);        m[i][j]=m[i][j-1]+nlay;
     ibig=0;    }
     del=0.0;    return m; 
     last_time=curr_time;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     (void) gettimeofday(&curr_time,&tzp);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     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);    */
     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++) {  /*************************free ma3x ************************/
       printf(" %d %.12f",i, p[i]);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       fprintf(ficlog," %d %.12lf",i, p[i]);  {
       fprintf(ficrespow," %.12lf", p[i]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     printf("\n");    free((FREE_ARG)(m+nrl-NR_END));
     fprintf(ficlog,"\n");  }
     fprintf(ficrespow,"\n");fflush(ficrespow);  
     if(*iter <=3){  /*************** function subdirf ***********/
       tm = *localtime(&curr_time.tv_sec);  char *subdirf(char fileres[])
       strcpy(strcurr,asctime(&tm));  {
 /*       asctime_r(&tm,strcurr); */    /* Caution optionfilefiname is hidden */
       forecast_time=curr_time;    strcpy(tmpout,optionfilefiname);
       itmp = strlen(strcurr);    strcat(tmpout,"/"); /* Add to the right */
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */    strcat(tmpout,fileres);
         strcurr[itmp-1]='\0';    return tmpout;
       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);  }
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);  
       for(niterf=10;niterf<=30;niterf+=10){  /*************** function subdirf2 ***********/
         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);  char *subdirf2(char fileres[], char *preop)
         tmf = *localtime(&forecast_time.tv_sec);  {
 /*      asctime_r(&tmf,strfor); */    
         strcpy(strfor,asctime(&tmf));    /* Caution optionfilefiname is hidden */
         itmp = strlen(strfor);    strcpy(tmpout,optionfilefiname);
         if(strfor[itmp-1]=='\n')    strcat(tmpout,"/");
         strfor[itmp-1]='\0';    strcat(tmpout,preop);
         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);    strcat(tmpout,fileres);
         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);    return tmpout;
       }  }
     }  
     for (i=1;i<=n;i++) {  /*************** function subdirf3 ***********/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char *subdirf3(char fileres[], char *preop, char *preop2)
       fptt=(*fret);  {
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);    /* Caution optionfilefiname is hidden */
       fprintf(ficlog,"fret=%lf \n",*fret);    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/");
       printf("%d",i);fflush(stdout);    strcat(tmpout,preop);
       fprintf(ficlog,"%d",i);fflush(ficlog);    strcat(tmpout,preop2);
       linmin(p,xit,n,fret,func);    strcat(tmpout,fileres);
       if (fabs(fptt-(*fret)) > del) {    return tmpout;
         del=fabs(fptt-(*fret));  }
         ibig=i;   
       }  /*************** function subdirfext ***********/
 #ifdef DEBUG  char *subdirfext(char fileres[], char *preop, char *postop)
       printf("%d %.12e",i,(*fret));  {
       fprintf(ficlog,"%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    strcpy(tmpout,preop);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    strcat(tmpout,fileres);
         printf(" x(%d)=%.12e",j,xit[j]);    strcat(tmpout,postop);
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    return tmpout;
       }  }
       for(j=1;j<=n;j++) {  
         printf(" p=%.12e",p[j]);  /*************** function subdirfext3 ***********/
         fprintf(ficlog," p=%.12e",p[j]);  char *subdirfext3(char fileres[], char *preop, char *postop)
       }  {
       printf("\n");    
       fprintf(ficlog,"\n");    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    strcat(tmpout,preop);
 #ifdef DEBUG    strcat(tmpout,fileres);
       int k[2],l;    strcat(tmpout,postop);
       k[0]=1;    return tmpout;
       k[1]=-1;  }
       printf("Max: %.12e",(*func)(p));   
       fprintf(ficlog,"Max: %.12e",(*func)(p));  char *asc_diff_time(long time_sec, char ascdiff[])
       for (j=1;j<=n;j++) {  {
         printf(" %.12e",p[j]);    long sec_left, days, hours, minutes;
         fprintf(ficlog," %.12e",p[j]);    days = (time_sec) / (60*60*24);
       }    sec_left = (time_sec) % (60*60*24);
       printf("\n");    hours = (sec_left) / (60*60) ;
       fprintf(ficlog,"\n");    sec_left = (sec_left) %(60*60);
       for(l=0;l<=1;l++) {    minutes = (sec_left) /60;
         for (j=1;j<=n;j++) {    sec_left = (sec_left) % (60);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    return ascdiff;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /***************** f1dim *************************/
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  extern int ncom; 
       }  extern double *pcom,*xicom;
 #endif  extern double (*nrfunc)(double []); 
    
   double f1dim(double x) 
       free_vector(xit,1,n);  { 
       free_vector(xits,1,n);    int j; 
       free_vector(ptt,1,n);    double f;
       free_vector(pt,1,n);    double *xt; 
       return;   
     }    xt=vector(1,ncom); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for (j=1;j<=n;j++) {    f=(*nrfunc)(xt); 
       ptt[j]=2.0*p[j]-pt[j];    free_vector(xt,1,ncom); 
       xit[j]=p[j]-pt[j];    return f; 
       pt[j]=p[j];  } 
     }  
     fptt=(*func)(ptt);  /*****************brent *************************/
     if (fptt < fp) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
         linmin(p,xit,n,fret,func);     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
         for (j=1;j<=n;j++) {     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
           xi[j][ibig]=xi[j][n];     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
           xi[j][n]=xit[j];     * returned function value. 
         }    */
 #ifdef DEBUG    int iter; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double a,b,d,etemp;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double fu=0,fv,fw,fx;
         for(j=1;j<=n;j++){    double ftemp=0.;
           printf(" %.12e",xit[j]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
           fprintf(ficlog," %.12e",xit[j]);    double e=0.0; 
         }   
         printf("\n");    a=(ax < cx ? ax : cx); 
         fprintf(ficlog,"\n");    b=(ax > cx ? ax : cx); 
 #endif    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
 }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /**** Prevalence limit (stable or period prevalence)  ****************/      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #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);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      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);
      matrix by transitions matrix until convergence is reached */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   int i, ii,j,k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double min, max, maxmin, maxmax,sumnew=0.;        *xmin=x; 
   double **matprod2();        return fx; 
   double **out, cov[NCOVMAX], **pmij();      } 
   double **newm;      ftemp=fu;
   double agefin, delaymax=50 ; /* Max number of years to converge */      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        q=(x-v)*(fx-fw); 
     for (j=1;j<=nlstate+ndeath;j++){        p=(x-v)*q-(x-w)*r; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
         q=fabs(q); 
    cov[1]=1.;        etemp=e; 
          e=d; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){                                  d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     newm=savm;        else { 
     /* Covariates have to be included here again */                                  d=p/q; 
      cov[2]=agefin;                                  u=x+d; 
                                    if (u-a < tol2 || b-u < tol2) 
       for (k=1; k<=cptcovn;k++) {                                          d=SIGN(tol1,xm-x); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        } 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      } else { 
       }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      } 
       for (k=1; k<=cptcovprod;k++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fu=(*f)(u); 
       if (fu <= fx) { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        if (u >= x) a=x; else b=x; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        SHFT(v,w,x,u) 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        SHFT(fv,fw,fx,fu) 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      } else { 
         if (u < x) a=u; else b=u; 
     savm=oldm;        if (fu <= fw || w == x) { 
     oldm=newm;                                  v=w; 
     maxmax=0.;                                  w=u; 
     for(j=1;j<=nlstate;j++){                                  fv=fw; 
       min=1.;                                  fw=fu; 
       max=0.;        } else if (fu <= fv || v == x || v == w) { 
       for(i=1; i<=nlstate; i++) {                                  v=u; 
         sumnew=0;                                  fv=fu; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        } 
         prlim[i][j]= newm[i][j]/(1-sumnew);      } 
         max=FMAX(max,prlim[i][j]);    } 
         min=FMIN(min,prlim[i][j]);    nrerror("Too many iterations in brent"); 
       }    *xmin=x; 
       maxmin=max-min;    return fx; 
       maxmax=FMAX(maxmax,maxmin);  } 
     }  
     if(maxmax < ftolpl){  /****************** mnbrak ***********************/
       return prlim;  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   }              double (*func)(double)) 
 }  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   the downhill direction (defined by the function as evaluated at the initial points) and returns
 /*************** transition probabilities ***************/  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
   values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )     */
 {    double ulim,u,r,q, dum;
   double s1, s2;    double fu; 
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    double scale=10.;
     int iterscale=0;
     for(i=1; i<= nlstate; i++){  
       for(j=1; j<i;j++){    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
           /*s2 += param[i][j][nc]*cov[nc];*/  
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
 /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
         }    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
         ps[i][j]=s2;    /*   *bx = *ax - (*ax - *bx)/scale; */
 /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
       }    /* } */
       for(j=i+1; j<=nlstate+ndeath;j++){  
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (*fb > *fa) { 
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      SHFT(dum,*ax,*bx,dum) 
 /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */      SHFT(dum,*fb,*fa,dum) 
         }    } 
         ps[i][j]=s2;    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
     }  #ifdef DEBUG
     /*ps[3][2]=1;*/    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
        fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
     for(i=1; i<= nlstate; i++){  #endif
       s1=0;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
       for(j=1; j<i; j++)      r=(*bx-*ax)*(*fb-*fc); 
         s1+=exp(ps[i][j]);      q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
       for(j=i+1; j<=nlstate+ndeath; j++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         s1+=exp(ps[i][j]);        (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[i][i]=1./(s1+1.);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
       for(j=1; j<i; j++)      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
         ps[i][j]= exp(ps[i][j])*ps[i][i];        fu=(*func)(u); 
       for(j=i+1; j<=nlstate+ndeath; j++)  #ifdef DEBUG
         ps[i][j]= exp(ps[i][j])*ps[i][i];        /* f(x)=A(x-u)**2+f(u) */
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        double A, fparabu; 
     } /* end i */        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
            fparabu= *fa - A*(*ax-u)*(*ax-u);
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
         ps[ii][jj]=0;        /* And thus,it can be that fu > *fc even if fparabu < *fc */
         ps[ii][ii]=1;        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
       }          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
     }        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
      #endif 
   #ifdef MNBRAKORIGINAL
 /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */  #else
 /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */  /*       if (fu > *fc) { */
 /*         printf("ddd %lf ",ps[ii][jj]); */  /* #ifdef DEBUG */
 /*       } */  /*       printf("mnbrak4  fu > fc \n"); */
 /*       printf("\n "); */  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
 /*        } */  /* #endif */
 /*        printf("\n ");printf("%lf ",cov[2]); */  /*      /\* 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(i=1; i<= npar; i++) printf("%f ",x[i]);  /*      dum=u; /\* Shifting c and u *\/ */
       goto end;*/  /*      u = *cx; */
     return ps;  /*      *cx = dum; */
 }  /*      dum = fu; */
   /*      fu = *fc; */
 /**************** Product of 2 matrices ******************/  /*      *fc =dum; */
   /*       } else { /\* end *\/ */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /* #ifdef DEBUG */
 {  /*       printf("mnbrak3  fu < fc \n"); */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /* #endif */
   /* in, b, out are matrice of pointers which should have been initialized  /*      dum=u; /\* Shifting c and u *\/ */
      before: only the contents of out is modified. The function returns  /*      u = *cx; */
      a pointer to pointers identical to out */  /*      *cx = dum; */
   long i, j, k;  /*      dum = fu; */
   for(i=nrl; i<= nrh; i++)  /*      fu = *fc; */
     for(k=ncolol; k<=ncoloh; k++)  /*      *fc =dum; */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*       } */
         out[i][k] +=in[i][j]*b[j][k];  #ifdef DEBUGMNBRAK
                    double A, fparabu; 
   return out;       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
 }       fparabu= *fa - A*(*ax-u)*(*ax-u);
        printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
        fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
 /************* Higher Matrix Product ***************/  #endif
         dum=u; /* Shifting c and u */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        u = *cx;
 {        *cx = dum;
   /* Computes the transition matrix starting at age 'age' over        dum = fu;
      'nhstepm*hstepm*stepm' months (i.e. until        fu = *fc;
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying        *fc =dum;
      nhstepm*hstepm matrices.  #endif
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
      (typically every 2 years instead of every month which is too big  #ifdef DEBUG
      for the memory).        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
      Model is determined by parameters x and covariates have to be        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
      included manually here.  #endif
         fu=(*func)(u); 
      */        if (fu < *fc) { 
   #ifdef DEBUG
   int i, j, d, h, k;                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
   double **out, cov[NCOVMAX];                            fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
   double **newm;  #endif
                             SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /* Hstepm could be zero and should return the unit matrix */                                  SHFT(*fb,*fc,fu,(*func)(u)) 
   for (i=1;i<=nlstate+ndeath;i++)  #ifdef DEBUG
     for (j=1;j<=nlstate+ndeath;j++){                                          printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
       oldm[i][j]=(i==j ? 1.0 : 0.0);  #endif
       po[i][j][0]=(i==j ? 1.0 : 0.0);        } 
     }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #ifdef DEBUG
   for(h=1; h <=nhstepm; h++){        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
     for(d=1; d <=hstepm; d++){        fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
       newm=savm;  #endif
       /* Covariates have to be included here again */        u=ulim; 
       cov[1]=1.;        fu=(*func)(u); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      } else { /* u could be left to b (if r > q parabola has a maximum) */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
       for (k=1; k<=cptcovage;k++)        printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
       for (k=1; k<=cptcovprod;k++)  #endif
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   #ifdef DEBUG
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      } /* end tests */
       savm=oldm;      SHFT(*ax,*bx,*cx,u) 
       oldm=newm;      SHFT(*fa,*fb,*fc,fu) 
     }  #ifdef DEBUG
     for(i=1; i<=nlstate+ndeath; i++)        printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
       for(j=1;j<=nlstate+ndeath;j++) {        fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
         po[i][j][h]=newm[i][j];  #endif
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
          */  } 
       }  
   } /* end h */  /*************** linmin ************************/
   return po;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
 }  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
 /*************** log-likelihood *************/  routines mnbrak and brent .*/
 double func( double *x)  int ncom; 
 {  double *pcom,*xicom;
   int i, ii, j, k, mi, d, kk;  double (*nrfunc)(double []); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];   
   double **out;  #ifdef LINMINORIGINAL
   double sw; /* Sum of weights */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double lli; /* Individual log likelihood */  #else
   int s1, s2;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
   double bbh, survp;  #endif
   long ipmx;  { 
   /*extern weight */    double brent(double ax, double bx, double cx, 
   /* We are differentiating ll according to initial status */                 double (*f)(double), double tol, double *xmin); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double f1dim(double x); 
   /*for(i=1;i<imx;i++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     printf(" %d\n",s[4][i]);                double *fc, double (*func)(double)); 
   */    int j; 
   cov[1]=1.;    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   #ifdef LINMINORIGINAL
   if(mle==1){  #else
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double scale=10., axs, xxs; /* Scale added for infinity */
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  #endif
       for(mi=1; mi<= wav[i]-1; mi++){    
         for (ii=1;ii<=nlstate+ndeath;ii++)    ncom=n; 
           for (j=1;j<=nlstate+ndeath;j++){    pcom=vector(1,n); 
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);    xicom=vector(1,n); 
             savm[ii][j]=(ii==j ? 1.0 : 0.0);    nrfunc=func; 
           }    for (j=1;j<=n;j++) { 
         for(d=0; d<dh[mi][i]; d++){      pcom[j]=p[j]; 
           newm=savm;      xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    } 
           for (kk=1; kk<=cptcovage;kk++) {  
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #ifdef LINMINORIGINAL
           }    xx=1.;
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #else
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    axs=0.0;
           savm=oldm;    xxs=1.;
           oldm=newm;    do{
         } /* end mult */      xx= xxs;
        #endif
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */      ax=0.;
         /* But now since version 0.9 we anticipate for bias at large stepm.      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
          * If stepm is larger than one month (smallest stepm) and if the exact delay      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
          * (in months) between two waves is not a multiple of stepm, we rounded to      /* 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))   */
          * the nearest (and in case of equal distance, to the lowest) interval but now      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
          * we keep into memory the bias bh[mi][i] and also the previous matrix product      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
          * probability in order to take into account the bias as a fraction of the way      /* 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]]*/
          * from savm to out if bh is negative or even beyond if bh is positive. bh varies  #ifdef LINMINORIGINAL
          * -stepm/2 to stepm/2 .  #else
          * For stepm=1 the results are the same as for previous versions of Imach.      if (fx != fx){
          * For stepm > 1 the results are less biased than in previous versions.                          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
          */                          printf("|");
         s1=s[mw[mi][i]][i];                          fprintf(ficlog,"|");
         s2=s[mw[mi+1][i]][i];  #ifdef DEBUGLINMIN
         bbh=(double)bh[mi][i]/(double)stepm;                          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);
         /* bias bh is positive if real duration  #endif
          * is higher than the multiple of stepm and negative otherwise.      }
          */    }while(fx != fx && xxs > 1.e-5);
         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/  #endif
         if( s2 > nlstate){    
           /* i.e. if s2 is a death state and if the date of death is known  #ifdef DEBUGLINMIN
              then the contribution to the likelihood is the probability to    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);
              die between last step unit time and current  step unit time,    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);
              which is also equal to probability to die before dh  #endif
              minus probability to die before dh-stepm .  #ifdef LINMINORIGINAL
              In version up to 0.92 likelihood was computed  #else
         as if date of death was unknown. Death was treated as any other          if(fb == fx){ /* Flat function in the direction */
         health state: the date of the interview describes the actual state                  xmin=xx;
         and not the date of a change in health state. The former idea was      *flat=1;
         to consider that at each interview the state was recorded          }else{
         (healthy, disable or death) and IMaCh was corrected; but when we      *flat=0;
         introduced the exact date of death then we should have modified  #endif
         the contribution of an exact death to the likelihood. This new                  /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
         contribution is smaller and very dependent of the step unit    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
         stepm. It is no more the probability to die between last interview    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
         and month of death but the probability to survive from last    /* fmin = f(p[j] + xmin * xi[j]) */
         interview up to one month before death multiplied by the    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
         probability to die within a month. Thanks to Chris    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
         Jackson for correcting this bug.  Former versions increased  #ifdef DEBUG
         mortality artificially. The bad side is that we add another loop    printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
         which slows down the processing. The difference can be up to 10%    fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
         lower mortality.  #endif
           */  #ifdef LINMINORIGINAL
           lli=log(out[s1][s2] - savm[s1][s2]);  #else
                           }
   #endif
         } else if  (s2==-2) {  #ifdef DEBUGLINMIN
           for (j=1,survp=0. ; j<=nlstate; j++)    printf("linmin end ");
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];    fprintf(ficlog,"linmin end ");
           /*survp += out[s1][j]; */  #endif
           lli= log(survp);    for (j=1;j<=n;j++) { 
         }  #ifdef LINMINORIGINAL
              xi[j] *= xmin; 
         else if  (s2==-4) {  #else
           for (j=3,survp=0. ; j<=nlstate; j++)    #ifdef DEBUGLINMIN
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];      if(xxs <1.0)
           lli= log(survp);        printf(" before xi[%d]=%12.8f", j,xi[j]);
         }  #endif
       xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
         else if  (s2==-5) {  #ifdef DEBUGLINMIN
           for (j=1,survp=0. ; j<=2; j++)        if(xxs <1.0)
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];        printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
           lli= log(survp);  #endif
         }  #endif
              p[j] += xi[j]; /* Parameters values are updated accordingly */
         else{    } 
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */  #ifdef DEBUGLINMIN
           /*  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");
         }    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/    fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
         /*if(lli ==000.0)*/    for (j=1;j<=n;j++) { 
         /*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); */      printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
         ipmx +=1;      fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
         sw += weight[i];      if(j % ncovmodel == 0){
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        printf("\n");
       } /* end of wave */        fprintf(ficlog,"\n");
     } /* end of individual */      }
   }  else if(mle==2){    }
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #else
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  #endif
       for(mi=1; mi<= wav[i]-1; mi++){    free_vector(xicom,1,n); 
         for (ii=1;ii<=nlstate+ndeath;ii++)    free_vector(pcom,1,n); 
           for (j=1;j<=nlstate+ndeath;j++){  } 
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
             savm[ii][j]=(ii==j ? 1.0 : 0.0);  
           }  /*************** powell ************************/
         for(d=0; d<=dh[mi][i]; d++){  /*
           newm=savm;  Minimization of a function func of n variables. Input consists of an initial starting point
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           for (kk=1; kk<=cptcovage;kk++) {  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  such that failure to decrease by more than this amount on one iteration signals doneness. On
           }  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  function value at p , and iter is the number of iterations taken. The routine linmin is used.
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));   */
           savm=oldm;  #ifdef LINMINORIGINAL
           oldm=newm;  #else
         } /* end mult */          int *flatdir; /* Function is vanishing in that direction */
                int flat=0; /* Function is vanishing in that direction */
         s1=s[mw[mi][i]][i];  #endif
         s2=s[mw[mi+1][i]][i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         bbh=(double)bh[mi][i]/(double)stepm;              double (*func)(double [])) 
         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */  { 
         ipmx +=1;  #ifdef LINMINORIGINAL
         sw += weight[i];   void linmin(double p[], double xi[], int n, double *fret, 
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;                double (*func)(double [])); 
       } /* end of wave */  #else 
     } /* end of individual */   void linmin(double p[], double xi[], int n, double *fret, 
   }  else if(mle==3){  /* exponential inter-extrapolation */                                                   double (*func)(double []),int *flat); 
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #endif
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    int i,ibig,j; 
       for(mi=1; mi<= wav[i]-1; mi++){    double del,t,*pt,*ptt,*xit;
         for (ii=1;ii<=nlstate+ndeath;ii++)    double directest;
           for (j=1;j<=nlstate+ndeath;j++){    double fp,fptt;
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double *xits;
             savm[ii][j]=(ii==j ? 1.0 : 0.0);    int niterf, itmp;
           }  #ifdef LINMINORIGINAL
         for(d=0; d<dh[mi][i]; d++){  #else
           newm=savm;  
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    flatdir=ivector(1,n); 
           for (kk=1; kk<=cptcovage;kk++) {    for (j=1;j<=n;j++) flatdir[j]=0; 
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #endif
           }  
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    pt=vector(1,n); 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    ptt=vector(1,n); 
           savm=oldm;    xit=vector(1,n); 
           oldm=newm;    xits=vector(1,n); 
         } /* end mult */    *fret=(*func)(p); 
          for (j=1;j<=n;j++) pt[j]=p[j]; 
         s1=s[mw[mi][i]][i];    rcurr_time = time(NULL);  
         s2=s[mw[mi+1][i]][i];    for (*iter=1;;++(*iter)) { 
         bbh=(double)bh[mi][i]/(double)stepm;      fp=(*fret); /* From former iteration or initial value */
         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 */      ibig=0; 
         ipmx +=1;      del=0.0; 
         sw += weight[i];      rlast_time=rcurr_time;
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      /* (void) gettimeofday(&curr_time,&tzp); */
       } /* end of wave */      rcurr_time = time(NULL);  
     } /* end of individual */      curr_time = *localtime(&rcurr_time);
   }else if (mle==4){  /* ml=4 no inter-extrapolation */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       for(mi=1; mi<= wav[i]-1; mi++){      for (i=1;i<=n;i++) {
         for (ii=1;ii<=nlstate+ndeath;ii++)        printf(" %d %.12f",i, p[i]);
           for (j=1;j<=nlstate+ndeath;j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficrespow," %.12lf", p[i]);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);      }
           }      printf("\n");
         for(d=0; d<dh[mi][i]; d++){      fprintf(ficlog,"\n");
           newm=savm;      fprintf(ficrespow,"\n");fflush(ficrespow);
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      if(*iter <=3){
           for (kk=1; kk<=cptcovage;kk++) {        tml = *localtime(&rcurr_time);
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        strcpy(strcurr,asctime(&tml));
           }        rforecast_time=rcurr_time; 
                itmp = strlen(strcurr);
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                  strcurr[itmp-1]='\0';
           savm=oldm;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           oldm=newm;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         } /* end mult */        for(niterf=10;niterf<=30;niterf+=10){
                                        rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         s1=s[mw[mi][i]][i];                                  forecast_time = *localtime(&rforecast_time);
         s2=s[mw[mi+1][i]][i];                                  strcpy(strfor,asctime(&forecast_time));
         if( s2 > nlstate){                                  itmp = strlen(strfor);
           lli=log(out[s1][s2] - savm[s1][s2]);                                  if(strfor[itmp-1]=='\n')
         }else{                                          strfor[itmp-1]='\0';
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */                                  printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         }                                  fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         ipmx +=1;        }
         sw += weight[i];      }
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for (i=1;i<=n;i++) { /* For each direction i */
 /*      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]); */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       } /* end of wave */        fptt=(*fret); 
     } /* end of individual */  #ifdef DEBUG
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  #endif
       for(mi=1; mi<= wav[i]-1; mi++){        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
         for (ii=1;ii<=nlstate+ndeath;ii++)        fprintf(ficlog,"%d",i);fflush(ficlog);
           for (j=1;j<=nlstate+ndeath;j++){  #ifdef LINMINORIGINAL
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
             savm[ii][j]=(ii==j ? 1.0 : 0.0);  #else
           }        linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
         for(d=0; d<dh[mi][i]; d++){                          flatdir[i]=flat; /* Function is vanishing in that direction i */
           newm=savm;  #endif
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;                          /* Outputs are fret(new point p) p is updated and xit rescaled */
           for (kk=1; kk<=cptcovage;kk++) {        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];                                  /* because that direction will be replaced unless the gain del is small */
           }                                  /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
                                          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                  /* with the new direction. */
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                  del=fabs(fptt-(*fret)); 
           savm=oldm;                                  ibig=i; 
           oldm=newm;        } 
         } /* end mult */  #ifdef DEBUG
              printf("%d %.12e",i,(*fret));
         s1=s[mw[mi][i]][i];        fprintf(ficlog,"%d %.12e",i,(*fret));
         s2=s[mw[mi+1][i]][i];        for (j=1;j<=n;j++) {
         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         ipmx +=1;                                  printf(" x(%d)=%.12e",j,xit[j]);
         sw += weight[i];                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         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]);*/        for(j=1;j<=n;j++) {
       } /* end of wave */                          printf(" p(%d)=%lf ",j,p[j]);
     } /* end of individual */                          fprintf(ficlog," p(%d)=%lf ",j,p[j]);
   } /* End of if */        }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        printf("\n");
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        fprintf(ficlog,"\n");
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  #endif
   return -l;      } /* end loop on each direction i */
 }      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
 /*************** log-likelihood *************/      /* New value of last point Pn is not computed, P(n-1) */
 double funcone( double *x)        for(j=1;j<=n;j++) {
 {                            printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
   /* Same as likeli but slower because of a lot of printf and if */                            fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
   int i, ii, j, k, mi, d, kk;        }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        printf("\n");
   double **out;        fprintf(ficlog,"\n");
   double lli; /* Individual log likelihood */  
   double llt;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   int s1, s2;        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
   double bbh, survp;        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
   /*extern weight */        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
   /* We are differentiating ll according to initial status */        /* decreased of more than 3.84  */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
   /*for(i=1;i<imx;i++)        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
     printf(" %d\n",s[4][i]);        /* By adding 10 parameters more the gain should be 18.31 */
   */                          
   cov[1]=1.;        /* 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 */
   for(k=1; k<=nlstate; k++) ll[k]=0.;        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
         /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #ifdef DEBUG
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        int k[2],l;
     for(mi=1; mi<= wav[i]-1; mi++){        k[0]=1;
       for (ii=1;ii<=nlstate+ndeath;ii++)        k[1]=-1;
         for (j=1;j<=nlstate+ndeath;j++){        printf("Max: %.12e",(*func)(p));
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficlog,"Max: %.12e",(*func)(p));
           savm[ii][j]=(ii==j ? 1.0 : 0.0);        for (j=1;j<=n;j++) {
         }          printf(" %.12e",p[j]);
       for(d=0; d<dh[mi][i]; d++){          fprintf(ficlog," %.12e",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];        for(l=0;l<=1;l++) {
         }          for (j=1;j<=n;j++) {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         savm=oldm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         oldm=newm;          }
       } /* end mult */          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)));
       s1=s[mw[mi][i]][i];        }
       s2=s[mw[mi+1][i]][i];  #endif
       bbh=(double)bh[mi][i]/(double)stepm;  
       /* bias is positive if real duration  #ifdef LINMINORIGINAL
        * is higher than the multiple of stepm and negative otherwise.  #else
        */        free_ivector(flatdir,1,n); 
       if( s2 > nlstate && (mle <5) ){  /* Jackson */  #endif
         lli=log(out[s1][s2] - savm[s1][s2]);        free_vector(xit,1,n); 
       } else if  (s2==-2) {        free_vector(xits,1,n); 
         for (j=1,survp=0. ; j<=nlstate; j++)        free_vector(ptt,1,n); 
           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];        free_vector(pt,1,n); 
         lli= log(survp);        return; 
       }else if (mle==1){      } /* enough precision */ 
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       } else if(mle==2){      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         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 */        ptt[j]=2.0*p[j]-pt[j]; 
       } else if(mle==3){  /* exponential inter-extrapolation */        xit[j]=p[j]-pt[j]; 
         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 */        pt[j]=p[j]; 
       } else if (mle==4){  /* mle=4 no inter-extrapolation */      } 
         lli=log(out[s1][s2]); /* Original formula */      fptt=(*func)(ptt); /* f_3 */
       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
         lli=log(out[s1][s2]); /* Original formula */                  if (*iter <=4) {
       } /* End of if */  #else                   
       ipmx +=1;  #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
       sw += weight[i];  #else
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
 /*       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]); */  #endif
       if(globpr){        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
  %11.6f %11.6f %11.6f ", \        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
           llt +=ll[k]*gipmx/gsw;        /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);        /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
         }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         fprintf(ficresilk," %10.6f\n", -llt);        /*  Even if f3 <f1, directest can be negative and t >0 */
       }        /* mu² and del² are equal when f3=f1 */
     } /* end of wave */                          /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
   } /* end of individual */                          /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];                          /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */                          /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  #ifdef NRCORIGINAL
   if(globpr==0){ /* First time we count the contributions and weights */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
     gipmx=ipmx;  #else
     gsw=sw;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
   }        t= t- del*SQR(fp-fptt);
   return -l;  #endif
 }        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
   #ifdef DEBUG
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
 /*************** function likelione ***********/        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);
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
 {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   /* This routine should help understanding what is done with        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
      the selection of individuals/waves and               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      to check the exact contribution to the likelihood.        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);
      Plotting could be done.        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
    */  #endif
   int k;  #ifdef POWELLORIGINAL
         if (t < 0.0) { /* Then we use it for new direction */
   if(*globpri !=0){ /* Just counts and sums, no printings */  #else
     strcpy(fileresilk,"ilk");        if (directest*t < 0.0) { /* Contradiction between both tests */
     strcat(fileresilk,fileres);                                  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);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       printf("Problem with resultfile: %s\n", fileresilk);          fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     }        } 
     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");        if (directest < 0.0) { /* Then we use it for new direction */
     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");  #endif
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */  #ifdef DEBUGLINMIN
     for(k=1; k<=nlstate; k++)                                  printf("Before linmin in direction P%d-P0\n",n);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);                                  for (j=1;j<=n;j++) {
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");                                          printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   }                                          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           if(j % ncovmodel == 0){
   *fretone=(*funcone)(p);                                                  printf("\n");
   if(*globpri !=0){                                                  fprintf(ficlog,"\n");
     fclose(ficresilk);                                          }
     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));                                  }
     fflush(fichtm);  #endif
   }  #ifdef LINMINORIGINAL
   return;                                  linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
 }  #else
                                   linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                                   flatdir[i]=flat; /* Function is vanishing in that direction i */
 /*********** Maximum Likelihood Estimation ***************/  #endif
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  #ifdef DEBUGLINMIN
 {                                  for (j=1;j<=n;j++) { 
   int i,j, iter;                                          printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   double **xi;                                          fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   double fret;                                          if(j % ncovmodel == 0){
   double fretone; /* Only one call to likelihood */                                                  printf("\n");
   /*  char filerespow[FILENAMELENGTH];*/                                                  fprintf(ficlog,"\n");
   xi=matrix(1,npar,1,npar);                                          }
   for (i=1;i<=npar;i++)                                  }
     for (j=1;j<=npar;j++)  #endif
       xi[i][j]=(i==j ? 1.0 : 0.0);                                  for (j=1;j<=n;j++) { 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");                                          xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
   strcpy(filerespow,"pow");                                          xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
   strcat(filerespow,fileres);                                  }
   if((ficrespow=fopen(filerespow,"w"))==NULL) {  #ifdef LINMINORIGINAL
     printf("Problem with resultfile: %s\n", filerespow);  #else
     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);                                  printf("Flat directions\n");
   }                                  fprintf(ficlog,"Flat directions\n");
   fprintf(ficrespow,"# Powell\n# iter -2*LL");                                  for (j=1;j<=n;j++) { 
   for (i=1;i<=nlstate;i++)                                          printf("flatdir[%d]=%d ",j,flatdir[j]);
     for(j=1;j<=nlstate+ndeath;j++)                                          fprintf(ficlog,"flatdir[%d]=%d ",j,flatdir[j]);
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);          }
   fprintf(ficrespow,"\n");                                  printf("\n");
                                   fprintf(ficlog,"\n");
   powell(p,xi,npar,ftol,&iter,&fret,func);  #endif
                                   printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   free_matrix(xi,1,npar,1,npar);                                  fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   fclose(ficrespow);                                  
   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  #ifdef DEBUG
   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));                                  printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));                                  fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                                   for(j=1;j<=n;j++){
 }                                          printf(" %lf",xit[j]);
                                           fprintf(ficlog," %lf",xit[j]);
 /**** Computes Hessian and covariance matrix ***/                                  }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))                                  printf("\n");
 {                                  fprintf(ficlog,"\n");
   double  **a,**y,*x,pd;  #endif
   double **hess;        } /* end of t or directest negative */
   int i, j,jk;  #ifdef POWELLNOF3INFF1TEST
   int *indx;  #else
       } /* end if (fptt < fp)  */
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);  #endif
   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);                  } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  #endif
   void ludcmp(double **a, int npar, int *indx, double *d) ;    } /* loop iteration */ 
   double gompertz(double p[]);  } 
   hess=matrix(1,npar,1,npar);  
   /**** Prevalence limit (stable or period prevalence)  ****************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
     fprintf(ficlog,"%d",i);fflush(ficlog);       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 */
      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);    /* Wx is row vector: population in state 1, population in state 2, population dead */
        /* or prevalence in state 1, prevalence in state 2, 0 */
     /*  printf(" %f ",p[i]);    /* newm is the matrix after multiplications, its rows are identical at a factor */
         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/    /* Initial matrix pimij */
   }    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
      /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   for (i=1;i<=npar;i++) {    /*  0,                   0                  , 1} */
     for (j=1;j<=npar;j++)  {    /*
       if (j>i) {     * and after some iteration: */
         printf(".%d%d",i,j);fflush(stdout);    /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
         hess[i][j]=hessij(p,delti,i,j,func,npar);    /*  0,                   0                  , 1} */
            /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
         hess[j][i]=hess[i][j];        /* {0.51571254859325999, 0.4842874514067399, */
         /*printf(" %lf ",hess[i][j]);*/    /*  0.51326036147820708, 0.48673963852179264} */
       }    /* If we start from prlim again, prlim tends to a constant matrix */
     }  
   }    int i, ii,j,k;
   printf("\n");    double *min, *max, *meandiff, maxmax,sumnew=0.;
   fprintf(ficlog,"\n");    /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double **newm;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
      int ncvloop=0;
   a=matrix(1,npar,1,npar);    
   y=matrix(1,npar,1,npar);    min=vector(1,nlstate);
   x=vector(1,npar);    max=vector(1,nlstate);
   indx=ivector(1,npar);    meandiff=vector(1,nlstate);
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /* Starting with matrix unity */
   ludcmp(a,npar,indx,&pd);    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   for (j=1;j<=npar;j++) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++) x[i]=0;      }
     x[j]=1;    
     lubksb(a,npar,indx,x);    cov[1]=1.;
     for (i=1;i<=npar;i++){    
       matcov[i][j]=x[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       ncvloop++;
   printf("\n#Hessian matrix#\n");      newm=savm;
   fprintf(ficlog,"\n#Hessian matrix#\n");      /* Covariates have to be included here again */
   for (i=1;i<=npar;i++) {      cov[2]=agefin;
     for (j=1;j<=npar;j++) {      if(nagesqr==1)
       printf("%.3e ",hess[i][j]);        cov[3]= agefin*agefin;;
       fprintf(ficlog,"%.3e ",hess[i][j]);      for (k=1; k<=cptcovn;k++) {
     }        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
     printf("\n");                          /* Here comes the value of the covariate 'ij' */
     fprintf(ficlog,"\n");        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
   }        /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
       }
   /* Recompute Inverse */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   for (i=1;i<=npar;i++)      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
   ludcmp(a,npar,indx,&pd);      for (k=1; k<=cptcovprod;k++) /* Useless */
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   /*  printf("\n#Hessian matrix recomputed#\n");        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
       
   for (j=1;j<=npar;j++) {      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (i=1;i<=npar;i++) x[i]=0;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     x[j]=1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     lubksb(a,npar,indx,x);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     for (i=1;i<=npar;i++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       y[i][j]=x[i];                  /* age and covariate values of ij are in 'cov' */
       printf("%.3e ",y[i][j]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       fprintf(ficlog,"%.3e ",y[i][j]);      
     }      savm=oldm;
     printf("\n");      oldm=newm;
     fprintf(ficlog,"\n");  
   }      for(j=1; j<=nlstate; j++){
   */        max[j]=0.;
         min[j]=1.;
   free_matrix(a,1,npar,1,npar);      }
   free_matrix(y,1,npar,1,npar);      for(i=1;i<=nlstate;i++){
   free_vector(x,1,npar);        sumnew=0;
   free_ivector(indx,1,npar);        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   free_matrix(hess,1,npar,1,npar);        for(j=1; j<=nlstate; j++){ 
           prlim[i][j]= newm[i][j]/(1-sumnew);
           max[j]=FMAX(max[j],prlim[i][j]);
 }          min[j]=FMIN(min[j],prlim[i][j]);
         }
 /*************** hessian matrix ****************/      }
 double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)  
 {      maxmax=0.;
   int i;      for(j=1; j<=nlstate; j++){
   int l=1, lmax=20;        meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
   double k1,k2;        maxmax=FMAX(maxmax,meandiff[j]);
   double p2[NPARMAX+1];        /* 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); */
   double res;      } /* j loop */
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;      *ncvyear= (int)age- (int)agefin;
   double fx;      /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
   int k=0,kmax=10;      if(maxmax < ftolpl){
   double l1;        /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
   fx=func(x);        free_vector(max,1,nlstate);
   for (i=1;i<=npar;i++) p2[i]=x[i];        free_vector(meandiff,1,nlstate);
   for(l=0 ; l <=lmax; l++){        return prlim;
     l1=pow(10,l);      }
     delts=delt;    } /* age loop */
     for(k=1 ; k <kmax; k=k+1){      /* After some age loop it doesn't converge */
       delt = delta*(l1*k);    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\
       p2[theta]=x[theta] +delt;  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);
       k1=func(p2)-fx;    /* 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); */
       p2[theta]=x[theta]-delt;    free_vector(min,1,nlstate);
       k2=func(p2)-fx;    free_vector(max,1,nlstate);
       /*res= (k1-2.0*fx+k2)/delt/delt; */    free_vector(meandiff,1,nlstate);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    
          return prlim; /* should not reach here */
 #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);  
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif   /**** Back Prevalence limit (stable or period prevalence)  ****************/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){   /* 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) */
         k=kmax;   /* 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)
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  {
         k=kmax; l=lmax*10.;    /* 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 */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
         delts=delt;    /* 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 */
   delti[theta]=delts;    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   return res;    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
      /*  0,                   0                  , 1} */
 }    /*
      * and after some iteration: */
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)    /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
 {    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
   int i;    /*  0,                   0                  , 1} */
   int l=1, l1, lmax=20;    /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
   double k1,k2,k3,k4,res,fx;    /* {0.51571254859325999, 0.4842874514067399, */
   double p2[NPARMAX+1];    /*  0.51326036147820708, 0.48673963852179264} */
   int k;    /* If we start from prlim again, prlim tends to a constant matrix */
   
   fx=func(x);    int i, ii,j,k;
   for (k=1; k<=2; k++) {    double *min, *max, *meandiff, maxmax,sumnew=0.;
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* double **matprod2(); */ /* test */
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **out, cov[NCOVMAX+1], **bmij();
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double **newm;
     k1=func(p2)-fx;    double         **dnewm, **doldm, **dsavm;  /* for use */
      double         **oldm, **savm;  /* for use */
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     k2=func(p2)-fx;    int ncvloop=0;
      
     p2[thetai]=x[thetai]-delti[thetai]/k;    min=vector(1,nlstate);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    max=vector(1,nlstate);
     k3=func(p2)-fx;    meandiff=vector(1,nlstate);
    
     p2[thetai]=x[thetai]-delti[thetai]/k;          dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          oldm=oldms; savm=savms;
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /* Starting with matrix unity */
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
     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+ndeath;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);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif      }
   }    
   return res;    cov[1]=1.;
 }    
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /************** Inverse of matrix **************/    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
 void ludcmp(double **a, int n, int *indx, double *d)    /* 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 */
   int i,imax,j,k;      ncvloop++;
   double big,dum,sum,temp;      newm=savm; /* oldm should be kept from previous iteration or unity at start */
   double *vv;                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
        /* Covariates have to be included here again */
   vv=vector(1,n);      cov[2]=agefin;
   *d=1.0;      if(nagesqr==1)
   for (i=1;i<=n;i++) {        cov[3]= agefin*agefin;;
     big=0.0;      for (k=1; k<=cptcovn;k++) {
     for (j=1;j<=n;j++)        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       if ((temp=fabs(a[i][j])) > big) big=temp;        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        /* 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])]); */
     vv[i]=1.0/big;      }
   }      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   for (j=1;j<=n;j++) {      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
     for (i=1;i<j;i++) {      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
       sum=a[i][j];      for (k=1; k<=cptcovprod;k++) /* Useless */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
       a[i][j]=sum;        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
     }      
     big=0.0;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (i=j;i<=n;i++) {      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       sum=a[i][j];      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for (k=1;k<j;k++)      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         sum -= a[i][k]*a[k][j];      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       a[i][j]=sum;                  /* ij should be linked to the correct index of cov */
       if ( (dum=vv[i]*fabs(sum)) >= big) {                  /* age and covariate values ij are in 'cov', but we need to pass
         big=dum;                   * ij for the observed prevalence at age and status and covariate
         imax=i;                   * number:  prevacurrent[(int)agefin][ii][ij]
       }                   */
     }      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
     if (j != imax) {      /* 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 *\/ */
       for (k=1;k<=n;k++) {      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
         dum=a[imax][k];      savm=oldm;
         a[imax][k]=a[j][k];      oldm=newm;
         a[j][k]=dum;      for(j=1; j<=nlstate; j++){
       }        max[j]=0.;
       *d = -(*d);        min[j]=1.;
       vv[imax]=vv[j];      }
     }      for(j=1; j<=nlstate; j++){ 
     indx[j]=imax;        for(i=1;i<=nlstate;i++){
     if (a[j][j] == 0.0) a[j][j]=TINY;                                  /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
     if (j != n) {                                  bprlim[i][j]= newm[i][j];
       dum=1.0/(a[j][j]);                                  max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;                                  min[i]=FMIN(min[i],bprlim[i][j]);
     }        }
   }      }
   free_vector(vv,1,n);  /* Doesn't work */                  
 ;      maxmax=0.;
 }      for(i=1; i<=nlstate; i++){
         meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
 void lubksb(double **a, int n, int *indx, double b[])        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); */
   int i,ii=0,ip,j;      } /* j loop */
   double sum;      *ncvyear= -( (int)age- (int)agefin);
        /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
   for (i=1;i<=n;i++) {      if(maxmax < ftolpl){
     ip=indx[i];        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
     sum=b[ip];        free_vector(min,1,nlstate);
     b[ip]=b[i];        free_vector(max,1,nlstate);
     if (ii)        free_vector(meandiff,1,nlstate);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        return bprlim;
     else if (sum) ii=i;      }
     b[i]=sum;    } /* age loop */
   }      /* After some age loop it doesn't converge */
   for (i=n;i>=1;i--) {    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\
     sum=b[i];  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);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[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); */
     b[i]=sum/a[i][i];    free_vector(min,1,nlstate);
   }    free_vector(max,1,nlstate);
 }    free_vector(meandiff,1,nlstate);
     
 void pstamp(FILE *fichier)    return bprlim; /* should not reach here */
 {  }
   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);  
 }  /*************** transition probabilities ***************/ 
   
 /************ Frequencies ********************/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 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 */    /* 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
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;       model to the ncovmodel covariates (including constant and age).
   int first;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   double ***freq; /* Frequencies */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   double *pp, **prop;       ncth covariate in the global vector x is given by the formula:
   double pos,posprop, k2, dateintsum=0,k2cpt=0;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   char fileresp[FILENAMELENGTH];       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   pp=vector(1,nlstate);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   prop=matrix(1,nlstate,iagemin,iagemax+3);       Outputs ps[i][j] the probability to be observed in j being in j according to
   strcpy(fileresp,"p");       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   strcat(fileresp,fileres);    */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double s1, lnpijopii;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /*double t34;*/
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    int i,j, nc, ii, jj;
     exit(0);  
   }    for(i=1; i<= nlstate; i++){
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);      for(j=1; j<i;j++){
   j1=0;        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
            /*lnpijopii += param[i][j][nc]*cov[nc];*/
   j=cptcoveff;          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
   first=1;        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   for(k1=1; k1<=j;k1++){      }
     for(i1=1; i1<=ncodemax[k1];i1++){      for(j=i+1; j<=nlstate+ndeath;j++){
       j1++;        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         scanf("%d", i);*/          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       for (i=-5; i<=nlstate+ndeath; i++)            /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         for (jk=-5; jk<=nlstate+ndeath; jk++)          }
           for(m=iagemin; m <= iagemax+3; m++)        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             freq[i][jk][m]=0;      }
     }
     for (i=1; i<=nlstate; i++)      
       for(m=iagemin; m <= iagemax+3; m++)    for(i=1; i<= nlstate; i++){
         prop[i][m]=0;      s1=0;
            for(j=1; j<i; j++){
       dateintsum=0;        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       k2cpt=0;        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for (i=1; i<=imx; i++) {      }
         bool=1;      for(j=i+1; j<=nlstate+ndeath; j++){
         if  (cptcovn>0) {        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           for (z1=1; z1<=cptcoveff; z1++)        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
               bool=0;      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         }      ps[i][i]=1./(s1+1.);
         if (bool==1){      /* Computing other pijs */
           for(m=firstpass; m<=lastpass; m++){      for(j=1; j<i; j++)
             k2=anint[m][i]+(mint[m][i]/12.);        ps[i][j]= exp(ps[i][j])*ps[i][i];
             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/      for(j=i+1; j<=nlstate+ndeath; j++)
               if(agev[m][i]==0) agev[m][i]=iagemax+1;        ps[i][j]= exp(ps[i][j])*ps[i][i];
               if(agev[m][i]==1) agev[m][i]=iagemax+2;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];    } /* end i */
               if (m<lastpass) {    
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];      for(jj=1; jj<= nlstate+ndeath; jj++){
               }        ps[ii][jj]=0;
                      ps[ii][ii]=1;
               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {      }
                 dateintsum=dateintsum+k2;    }
                 k2cpt++;    
               }    
               /*}*/    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           }    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         }    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       }    /*   } */
            /*   printf("\n "); */
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/    /* } */
       pstamp(ficresp);    /* printf("\n ");printf("%lf ",cov[2]);*/
       if  (cptcovn>0) {    /*
         fprintf(ficresp, "\n#********** Variable ");      for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                  goto end;*/
         fprintf(ficresp, "**********\n#");    return ps;
       }  }
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*************** backward transition probabilities ***************/ 
       fprintf(ficresp, "\n");  
         /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
       for(i=iagemin; i <= iagemax+3; i++){  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
         if(i==iagemax+3){   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
           fprintf(ficlog,"Total");  {
         }else{    /* Computes the backward probability at age agefin and covariate ij
           if(first==1){     * and returns in **ps as well as **bmij.
             first=0;     */
             printf("See log file for details...\n");    int i, ii, j,k;
           }    
           fprintf(ficlog,"Age %d", i);    double **out, **pmij();
         }    double sumnew=0.;
         for(jk=1; jk <=nlstate ; jk++){    double agefin;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    
             pp[jk] += freq[jk][m][i];    double **dnewm, **dsavm, **doldm;
         }    double **bbmij;
         for(jk=1; jk <=nlstate ; jk++){    
           for(m=-1, pos=0; m <=0 ; m++)    doldm=ddoldms; /* global pointers */
             pos += freq[jk][m][i];    dnewm=ddnewms;
           if(pp[jk]>=1.e-10){    dsavm=ddsavms;
             if(first==1){    
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    agefin=cov[2];
             }    /* bmij *//* age is cov[2], ij is included in cov, but we need for
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       the observed prevalence (with this covariate ij) */
           }else{    dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
             if(first==1)    /* We do have the matrix Px in savm  and we need pij */
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=1;j<=nlstate+ndeath;j++){
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      sumnew=0.; /* w1 p11 + w2 p21 only on live states */
           }      for (ii=1;ii<=nlstate;ii++){
         }        sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
       } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
         for(jk=1; jk <=nlstate ; jk++){      for (ii=1;ii<=nlstate+ndeath;ii++){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        if(sumnew >= 1.e-10){
             pp[jk] += freq[jk][m][i];          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
         }                /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
           pos += pp[jk];          /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           posprop += prop[jk][i];          /* }else */
         }          doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
         for(jk=1; jk <=nlstate ; jk++){        }else{
           if(pos>=1.e-5){          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);
             if(first==1)        }
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } /*End ii */
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
           }else{    /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
             if(first==1)    bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
           }    /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
           if( i <= iagemax){    /* left Product of this matrix by diag matrix of prevalences (savm) */
             if(pos>=1.e-5){    for (j=1;j<=nlstate+ndeath;j++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);      for (ii=1;ii<=nlstate+ndeath;ii++){
               /*probs[i][jk][j1]= pp[jk]/pos;*/        dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      }
             }    } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
             else    ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);    /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
           }    /* end bmij */
         }    return ps; 
          }
         for(jk=-1; jk <=nlstate+ndeath; jk++)  /*************** transition probabilities ***************/ 
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) {  double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
             if(first==1)  {
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    /* According to parameters values stored in x and the covariate's values stored in cov,
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);       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).
         if(i <= iagemax)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           fprintf(ficresp,"\n");       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         if(first==1)       ncth covariate in the global vector x is given by the formula:
           printf("Others in log...\n");       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         fprintf(ficlog,"\n");       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     }       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   }       Outputs ps[i][j] the probability to be observed in j being in j according to
   dateintmean=dateintsum/k2cpt;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
      */
   fclose(ficresp);    double s1, lnpijopii;
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);    /*double t34;*/
   free_vector(pp,1,nlstate);    int i,j, nc, ii, jj;
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);  
   /* End of Freq */          for(i=1; i<= nlstate; i++){
 }                  for(j=1; j<i;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 /************ Prevalence ********************/                                  /*lnpijopii += param[i][j][nc]*cov[nc];*/
 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)                                  lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
 {                                    /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   /* 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).                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      We still use firstpass and lastpass as another selection.                          /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   */                  }
                    for(j=i+1; j<=nlstate+ndeath;j++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;                          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   double ***freq; /* Frequencies */                                  /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   double *pp, **prop;                                  lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   double pos,posprop;                                  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   double  y2; /* in fractional years */                          }
   int iagemin, iagemax;                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   }
   iagemin= (int) agemin;          }
   iagemax= (int) agemax;          
   /*pp=vector(1,nlstate);*/          for(i=1; i<= nlstate; i++){
   prop=matrix(1,nlstate,iagemin,iagemax+3);                  s1=0;
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/                  for(j=1; j<i; j++){
   j1=0;                          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); */
   j=cptcoveff;                  }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}                  for(j=i+1; j<=nlstate+ndeath; j++){
                            s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   for(k1=1; k1<=j;k1++){                          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(i1=1; i1<=ncodemax[k1];i1++){                  }
       j1++;                  /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                        ps[i][i]=1./(s1+1.);
       for (i=1; i<=nlstate; i++)                    /* Computing other pijs */
         for(m=iagemin; m <= iagemax+3; m++)                  for(j=1; j<i; j++)
           prop[i][m]=0.0;                          ps[i][j]= exp(ps[i][j])*ps[i][i];
                        for(j=i+1; j<=nlstate+ndeath; j++)
       for (i=1; i<=imx; i++) { /* Each individual */                          ps[i][j]= exp(ps[i][j])*ps[i][i];
         bool=1;                  /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if  (cptcovn>0) {          } /* end i */
           for (z1=1; z1<=cptcoveff; z1++)          
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
               bool=0;                  for(jj=1; jj<= nlstate+ndeath; jj++){
         }                          ps[ii][jj]=0;
         if (bool==1) {                          ps[ii][ii]=1;
           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/                  }
             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */          }
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */          /* Added for backcast */ /* Transposed matrix too */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;          for(jj=1; jj<= nlstate+ndeath; jj++){
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                  s1=0.;
               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);                  for(ii=1; ii<= nlstate+ndeath; ii++){
               if (s[m][i]>0 && s[m][i]<=nlstate) {                          s1+=ps[ii][jj];
                 /*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];                  for(ii=1; ii<= nlstate; ii++){
                 prop[s[m][i]][iagemax+3] += weight[i];                          ps[ii][jj]=ps[ii][jj]/s1;
               }                  }
             }          }
           } /* end selection of waves */          /* Transposition */
         }          for(jj=1; jj<= nlstate+ndeath; jj++){
       }                  for(ii=jj; ii<= nlstate+ndeath; ii++){
       for(i=iagemin; i <= iagemax+3; i++){                            s1=ps[ii][jj];
                                  ps[ii][jj]=ps[jj][ii];
         for(jk=1,posprop=0; jk <=nlstate ; jk++) {                          ps[jj][ii]=s1;
           posprop += prop[jk][i];                  }
         }          }
           /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         for(jk=1; jk <=nlstate ; jk++){              /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           if( i <=  iagemax){          /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
             if(posprop>=1.e-5){          /*   } */
               probs[i][jk][j1]= prop[jk][i]/posprop;          /*   printf("\n "); */
             }          /* } */
           }          /* printf("\n ");printf("%lf ",cov[2]);*/
         }/* end jk */          /*
       }/* end i */                  for(i=1; i<= npar; i++) printf("%f ",x[i]);
     } /* end i1 */                  goto end;*/
   } /* end k1 */          return ps;
    }
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/  
   /*free_vector(pp,1,nlstate);*/  
   free_matrix(prop,1,nlstate, iagemin,iagemax+3);  /**************** Product of 2 matrices ******************/
 }  /* End of prevalence */  
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 /************* Waves Concatenation ***************/  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 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)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 {    /* in, b, out are matrice of pointers which should have been initialized 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.       before: only the contents of out is modified. The function returns
      Death is a valid wave (if date is known).       a pointer to pointers identical to out */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    int i, j, k;
      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]    for(i=nrl; i<= nrh; i++)
      and mw[mi+1][i]. dh depends on stepm.      for(k=ncolol; k<=ncoloh; k++){
      */        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
   int i, mi, m;          out[i][k] +=in[i][j]*b[j][k];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      }
      double sum=0., jmean=0.;*/    return out;
   int first;  }
   int j, k=0,jk, ju, jl;  
   double sum=0.;  
   first=0;  /************* Higher Matrix Product ***************/
   jmin=1e+5;  
   jmax=-1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   jmean=0.;  {
   for(i=1; i<=imx; i++){    /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
     mi=0;       'nhstepm*hstepm*stepm' months (i.e. until
     m=firstpass;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     while(s[m][i] <= nlstate){       nhstepm*hstepm matrices. 
       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         mw[++mi][i]=m;       (typically every 2 years instead of every month which is too big 
       if(m >=lastpass)       for the memory).
         break;       Model is determined by parameters x and covariates have to be 
       else       included manually here. 
         m++;  
     }/* end while */       */
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */    int i, j, d, h, k;
       /* if(mi==0)  never been interviewed correctly before death */    double **out, cov[NCOVMAX+1];
          /* Only death is a correct wave */    double **newm;
       mw[mi][i]=m;    double agexact;
     }    double agebegin, ageend;
   
     wav[i]=mi;    /* Hstepm could be zero and should return the unit matrix */
     if(mi==0){    for (i=1;i<=nlstate+ndeath;i++)
       nbwarn++;      for (j=1;j<=nlstate+ndeath;j++){
       if(first==0){        oldm[i][j]=(i==j ? 1.0 : 0.0);
         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);        po[i][j][0]=(i==j ? 1.0 : 0.0);
         first=1;      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       if(first==1){    for(h=1; h <=nhstepm; h++){
         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);      for(d=1; d <=hstepm; d++){
       }        newm=savm;
     } /* end mi==0 */        /* Covariates have to be included here again */
   } /* End individuals */        cov[1]=1.;
         agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
   for(i=1; i<=imx; i++){        cov[2]=agexact;
     for(mi=1; mi<wav[i];mi++){        if(nagesqr==1)
       if (stepm <=0)                                  cov[3]= agexact*agexact;
         dh[mi][i]=1;        for (k=1; k<=cptcovn;k++) 
       else{                                  cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */                          /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
           if (agedc[i] < 2*AGESUP) {        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                                  /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
             if(j==0) j=1;  /* Survives at least one month after exam */                                  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
             else if(j<0){                          /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
               nberr++;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
               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]);                                  cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
               j=1; /* Temporary Dangerous patch */                          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);  
               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);  
               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
             }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             k=k+1;                          /* right multiplication of oldm by the current matrix */
             if (j >= jmax){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
               jmax=j;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               ijmax=i;        /* if((int)age == 70){ */
             }        /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
             if (j <= jmin){        /*        for(i=1; i<=nlstate+ndeath; i++) { */
               jmin=j;        /*          printf("%d pmmij ",i); */
               ijmin=i;        /*          for(j=1;j<=nlstate+ndeath;j++) { */
             }        /*            printf("%f ",pmmij[i][j]); */
             sum=sum+j;        /*          } */
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/        /*          printf(" oldm "); */
             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/        /*          for(j=1;j<=nlstate+ndeath;j++) { */
           }        /*            printf("%f ",oldm[i][j]); */
         }        /*          } */
         else{        /*          printf("\n"); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        /*        } */
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */        /* } */
         savm=oldm;
           k=k+1;        oldm=newm;
           if (j >= jmax) {      }
             jmax=j;      for(i=1; i<=nlstate+ndeath; i++)
             ijmax=i;        for(j=1;j<=nlstate+ndeath;j++) {
           }                                  po[i][j][h]=newm[i][j];
           else if (j <= jmin){                                  /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
             jmin=j;        }
             ijmin=i;      /*printf("h=%d ",h);*/
           }    } /* end h */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          /*     printf("\n H=%d \n",h); */
           /*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]);*/    return po;
           if(j<0){  }
             nberr++;  
             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);  /************* Higher Back Matrix Product ***************/
             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]);  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
           }  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
           sum=sum+j;  {
         }    /* Computes the transition matrix starting at age 'age' over
         jk= j/stepm;       'nhstepm*hstepm*stepm' months (i.e. until
         jl= j -jk*stepm;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
         ju= j -(jk+1)*stepm;       nhstepm*hstepm matrices.
         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step
           if(jl==0){       (typically every 2 years instead of every month which is too big
             dh[mi][i]=jk;       for the memory).
             bh[mi][i]=0;       Model is determined by parameters x and covariates have to be
           }else{ /* We want a negative bias in order to only have interpolation ie       included manually here.
                   * at the price of an extra matrix product in likelihood */  
             dh[mi][i]=jk+1;    */
             bh[mi][i]=ju;  
           }    int i, j, d, h, k;
         }else{    double **out, cov[NCOVMAX+1];
           if(jl <= -ju){    double **newm;
             dh[mi][i]=jk;    double agexact;
             bh[mi][i]=jl;       /* bias is positive if real duration    double agebegin, ageend;
                                  * is higher than the multiple of stepm and negative otherwise.    double **oldm, **savm;
                                  */  
           }    oldm=oldms;savm=savms;
           else{    /* Hstepm could be zero and should return the unit matrix */
             dh[mi][i]=jk+1;    for (i=1;i<=nlstate+ndeath;i++)
             bh[mi][i]=ju;      for (j=1;j<=nlstate+ndeath;j++){
           }        oldm[i][j]=(i==j ? 1.0 : 0.0);
           if(dh[mi][i]==0){        po[i][j][0]=(i==j ? 1.0 : 0.0);
             dh[mi][i]=1; /* At least one step */      }
             bh[mi][i]=ju; /* At least one step */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             /*  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);*/    for(h=1; h <=nhstepm; h++){
           }      for(d=1; d <=hstepm; d++){
         } /* end if mle */        newm=savm;
       }        /* Covariates have to be included here again */
     } /* end wave */        cov[1]=1.;
   }        agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
   jmean=sum/k;        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
   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);        cov[2]=agexact;
   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(nagesqr==1)
  }          cov[3]= agexact*agexact;
         for (k=1; k<=cptcovn;k++)
 /*********** Tricode ****************************/          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
 void tricode(int *Tvar, int **nbcode, int imx)        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
 {        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
            /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   int Ndum[20],ij=1, k, j, i, maxncov=19;          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
   int cptcode=0;        /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
   cptcoveff=0;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
   for (k=0; k<maxncov; k++) Ndum[k]=0;        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   for (k=1; k<=7; k++) ncodemax[k]=0;                          
                           
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                                modality*/        /* Careful transposed matrix */
       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/        /* age is in cov[2] */
       Ndum[ij]++; /*store the modality */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                                        Tvar[j]. If V=sex and male is 0 and                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                                        female is 1, then  cptcode=1.*/        /* if((int)age == 70){ */
     }        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
     for (i=0; i<=cptcode; i++) {        /*          printf("%d pmmij ",i); */
       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 */        /*          for(j=1;j<=nlstate+ndeath;j++) { */
     }        /*            printf("%f ",pmmij[i][j]); */
         /*          } */
     ij=1;        /*          printf(" oldm "); */
     for (i=1; i<=ncodemax[j]; i++) {        /*          for(j=1;j<=nlstate+ndeath;j++) { */
       for (k=0; k<= maxncov; k++) {        /*            printf("%f ",oldm[i][j]); */
         if (Ndum[k] != 0) {        /*          } */
           nbcode[Tvar[j]][ij]=k;        /*          printf("\n"); */
           /* 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; */        /*        } */
                  /* } */
           ij++;        savm=oldm;
         }        oldm=newm;
         if (ij > ncodemax[j]) break;      }
       }        for(i=1; i<=nlstate+ndeath; i++)
     }        for(j=1;j<=nlstate+ndeath;j++) {
   }            po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
  for (k=0; k< maxncov; k++) Ndum[k]=0;        }
       /*printf("h=%d ",h);*/
  for (i=1; i<=ncovmodel-2; i++) {    } /* end h */
    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/    /*     printf("\n H=%d \n",h); */
    ij=Tvar[i];    return po;
    Ndum[ij]++;  }
  }  
   
  ij=1;  #ifdef NLOPT
  for (i=1; i<= maxncov; i++) {    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    if((Ndum[i]!=0) && (i<=ncovcol)){    double fret;
      Tvaraff[ij]=i; /*For printing */    double *xt;
      ij++;    int j;
    }    myfunc_data *d2 = (myfunc_data *) pd;
  }  /* xt = (p1-1); */
      xt=vector(1,n); 
  cptcoveff=ij-1; /*Number of simple covariates*/    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
 }  
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
 /*********** Health Expectancies ****************/    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
 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[] )    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
 {   free_vector(xt,1,n);
   /* Health expectancies, no variances */    return fret;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;  }
   double age, agelim, hf;  #endif
   double ***p3mat;  
   double eip;  /*************** log-likelihood *************/
   double func( double *x)
   pstamp(ficreseij);  {
   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");          int i, ii, j, k, mi, d, kk;
   fprintf(ficreseij,"# Age");          int ioffset=0;
   for(i=1; i<=nlstate;i++){          double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(j=1; j<=nlstate;j++){          double **out;
       fprintf(ficreseij," e%1d%1d ",i,j);          double sw; /* Sum of weights */
     }          double lli; /* Individual log likelihood */
     fprintf(ficreseij," e%1d. ",i);          int s1, s2;
   }          int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   fprintf(ficreseij,"\n");          double bbh, survp;
           long ipmx;
            double agexact;
   if(estepm < stepm){          /*extern weight */
     printf ("Problem %d lower than %d\n",estepm, stepm);          /* We are differentiating ll according to initial status */
   }          /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   else  hstepm=estepm;            /*for(i=1;i<imx;i++) 
   /* We compute the life expectancy from trapezoids spaced every estepm months                  printf(" %d\n",s[4][i]);
    * This is mainly to measure the difference between two models: for example          */
    * if stepm=24 months pijx are given only every 2 years and by summing them  
    * we are calculating an estimate of the Life Expectancy assuming a linear          ++countcallfunc;
    * progression in between and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we          cov[1]=1.;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  
    * to compare the new estimate of Life expectancy with the same linear          for(k=1; k<=nlstate; k++) ll[k]=0.;
    * hypothesis. A more precise result, taking into account a more precise    ioffset=0;
    * curvature will be obtained if estepm is as small as stepm. */          if(mle==1){
                   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* For example we decided to compute the life expectancy with the smallest unit */                          /* Computes the values of the ncovmodel covariates of the model
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                                   depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
      nhstepm is the number of hstepm from age to agelim                                   Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
      nstepm is the number of stepm from age to agelin.                                   to be observed in j being in i according to the model.
      Look at hpijx to understand the reason of that which relies in memory size                          */
      and note for a fixed period like estepm months */                          ioffset=2+nagesqr+cptcovage;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                          /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
      survival function given by stepm (the optimization length). Unfortunately it                          for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
      means that if the survival funtion is printed only each two years of age and if                                  cov[++ioffset]=covar[Tvar[k]][i];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                          }
      results. So we changed our mind and took the option of the best precision.                          for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
   */                                  cov[++ioffset]=coqvar[iqv][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                          }
   
   agelim=AGESUP;                          /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   /* If stepm=6 months */                                   is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                                   has been calculated etc */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                          /* For an individual i, wav[i] gives the number of effective waves */
                              /* We compute the contribution to Likelihood of each effective transition
 /* nhstepm age range expressed in number of stepm */                                   mw[mi][i] is real wave of the mi th effectve wave */
   nstepm=(int) rint((agelim-bage)*YEARM/stepm);                          /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
   /* Typically if 20 years nstepm = 20*12/6=40 stepm */                                   s2=s[mw[mi+1][i]][i];
   /* if (stepm >= YEARM) hstepm=1;*/                                   And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                                   But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
                           */
   for (age=bage; age<=fage; age ++){                          for(mi=1; mi<= wav[i]-1; mi++){
                                   for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
                                           cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);                                    }
                                      for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                                          cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
                                      }
     printf("%d|",(int)age);fflush(stdout);                                  /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);                                  for (ii=1;ii<=nlstate+ndeath;ii++)
                                              for (j=1;j<=nlstate+ndeath;j++){
                                                   oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computing expectancies */                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)                                          }
       for(j=1; j<=nlstate;j++)                                  for(d=0; d<dh[mi][i]; d++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                                          newm=savm;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                                    cov[2]=agexact;
           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/                                          if(nagesqr==1)
                                                   cov[3]= agexact*agexact;  /* Should be changed here */
         }                                          for (kk=1; kk<=cptcovage;kk++) {
                                                      cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
     fprintf(ficreseij,"%3.0f",age );                                          }
     for(i=1; i<=nlstate;i++){                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       eip=0;                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++){                                          savm=oldm;
         eip +=eij[i][j][(int)age];                                          oldm=newm;
         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );                                  } /* end mult */
       }                                  
       fprintf(ficreseij,"%9.4f", eip );                                          /*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.
     fprintf(ficreseij,"\n");                                   * If stepm is larger than one month (smallest stepm) and if the exact delay 
                                       * (in months) between two waves is not a multiple of stepm, we rounded to 
   }                                   * the nearest (and in case of equal distance, to the lowest) interval but now
   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   * we keep into memory the bias bh[mi][i] and also the previous matrix product
   printf("\n");                                   * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   fprintf(ficlog,"\n");                                   * probability in order to take into account the bias as a fraction of the way
                                     * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 }                                   * -stepm/2 to stepm/2 .
                                    * For stepm=1 the results are the same as for previous versions of Imach.
 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[] )                                   * For stepm > 1 the results are less biased than in previous versions. 
                                    */
 {                                  s1=s[mw[mi][i]][i];
   /* Covariances of health expectancies eij and of total life expectancies according                                  s2=s[mw[mi+1][i]][i];
    to initial status i, ei. .                                  bbh=(double)bh[mi][i]/(double)stepm; 
   */                                  /* bias bh is positive if real duration
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;                                   * is higher than the multiple of stepm and negative otherwise.
   double age, agelim, hf;                                   */
   double ***p3matp, ***p3matm, ***varhe;                                  /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double **dnewm,**doldm;                                  if( s2 > nlstate){ 
   double *xp, *xm;                                          /* i.e. if s2 is a death state and if the date of death is known 
   double **gp, **gm;                                                   then the contribution to the likelihood is the probability to 
   double ***gradg, ***trgradg;                                                   die between last step unit time and current  step unit time, 
   int theta;                                                   which is also equal to probability to die before dh 
                                                    minus probability to die before dh-stepm . 
   double eip, vip;                                                   In version up to 0.92 likelihood was computed
                                                    as if date of death was unknown. Death was treated as any other
   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);                                                   health state: the date of the interview describes the actual state
   xp=vector(1,npar);                                                   and not the date of a change in health state. The former idea was
   xm=vector(1,npar);                                                   to consider that at each interview the state was recorded
   dnewm=matrix(1,nlstate*nlstate,1,npar);                                                   (healthy, disable or death) and IMaCh was corrected; but when we
   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);                                                   introduced the exact date of death then we should have modified
                                                     the contribution of an exact death to the likelihood. This new
   pstamp(ficresstdeij);                                                   contribution is smaller and very dependent of the step unit
   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");                                                   stepm. It is no more the probability to die between last interview
   fprintf(ficresstdeij,"# Age");                                                   and month of death but the probability to survive from last
   for(i=1; i<=nlstate;i++){                                                   interview up to one month before death multiplied by the
     for(j=1; j<=nlstate;j++)                                                   probability to die within a month. Thanks to Chris
       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);                                                   Jackson for correcting this bug.  Former versions increased
     fprintf(ficresstdeij," e%1d. ",i);                                                   mortality artificially. The bad side is that we add another loop
   }                                                   which slows down the processing. The difference can be up to 10%
   fprintf(ficresstdeij,"\n");                                                   lower mortality.
                                           */
   pstamp(ficrescveij);                                          /* If, at the beginning of the maximization mostly, the
   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");                                                   cumulative probability or probability to be dead is
   fprintf(ficrescveij,"# Age");                                                   constant (ie = 1) over time d, the difference is equal to
   for(i=1; i<=nlstate;i++)                                                   0.  out[s1][3] = savm[s1][3]: probability, being at state
     for(j=1; j<=nlstate;j++){                                                   s1 at precedent wave, to be dead a month before current
       cptj= (j-1)*nlstate+i;                                                   wave is equal to probability, being at state s1 at
       for(i2=1; i2<=nlstate;i2++)                                                   precedent wave, to be dead at mont of the current
         for(j2=1; j2<=nlstate;j2++){                                                   wave. Then the observed probability (that this person died)
           cptj2= (j2-1)*nlstate+i2;                                                   is null according to current estimated parameter. In fact,
           if(cptj2 <= cptj)                                                   it should be very low but not zero otherwise the log go to
             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);                                                   infinity.
         }                                          */
     }  /* #ifdef INFINITYORIGINAL */
   fprintf(ficrescveij,"\n");  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
    /* #else */
   if(estepm < stepm){  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
     printf ("Problem %d lower than %d\n",estepm, stepm);  /*          lli=log(mytinydouble); */
   }  /*        else */
   else  hstepm=estepm;    /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* We compute the life expectancy from trapezoids spaced every estepm months  /* #endif */
    * This is mainly to measure the difference between two models: for example                                          lli=log(out[s1][s2] - savm[s1][s2]);
    * if stepm=24 months pijx are given only every 2 years and by summing them            
    * we are calculating an estimate of the Life Expectancy assuming a linear                                  } else if  ( s2==-1 ) { /* alive */
    * progression in between and thus overestimating or underestimating according                                          for (j=1,survp=0. ; j<=nlstate; j++) 
    * to the curvature of the survival function. If, for the same date, we                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                                          /*survp += out[s1][j]; */
    * to compare the new estimate of Life expectancy with the same linear                                          lli= log(survp);
    * hypothesis. A more precise result, taking into account a more precise                                  }
    * curvature will be obtained if estepm is as small as stepm. */                                  else if  (s2==-4) { 
                                           for (j=3,survp=0. ; j<=nlstate; j++)  
   /* For example we decided to compute the life expectancy with the smallest unit */                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                                          lli= log(survp); 
      nhstepm is the number of hstepm from age to agelim                                  } 
      nstepm is the number of stepm from age to agelin.                                  else if  (s2==-5) { 
      Look at hpijx to understand the reason of that which relies in memory size                                          for (j=1,survp=0. ; j<=2; j++)  
      and note for a fixed period like estepm months */                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                                          lli= log(survp); 
      survival function given by stepm (the optimization length). Unfortunately it                                  } 
      means that if the survival funtion is printed only each two years of age and if                                  else{
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                                          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      results. So we changed our mind and took the option of the best precision.                                          /*  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 */
   */                                  } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                                  /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                                   /*if(lli ==000.0)*/
   /* If stepm=6 months */                                  /*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 age range expressed in number of stepm */                                  ipmx +=1;
   agelim=AGESUP;                                  sw += weight[i];
   nstepm=(int) rint((agelim-bage)*YEARM/stepm);                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Typically if 20 years nstepm = 20*12/6=40 stepm */                                  /* if (lli < log(mytinydouble)){ */
   /* if (stepm >= YEARM) hstepm=1;*/                                  /*   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); */
   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                                  /*   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]); */
                                    /* } */
   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                          } /* end of wave */
   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  } /* end of individual */
   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);          }  else if(mle==2){
   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   gp=matrix(0,nhstepm,1,nlstate*nlstate);                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   gm=matrix(0,nhstepm,1,nlstate*nlstate);                          for(mi=1; mi<= wav[i]-1; mi++){
                                   for (ii=1;ii<=nlstate+ndeath;ii++)
   for (age=bage; age<=fage; age ++){                                          for (j=1;j<=nlstate+ndeath;j++){
                                                   oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                                          }
                                    for(d=0; d<=dh[mi][i]; d++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                                          newm=savm;
                                           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Computing  Variances of health expectancies */                                          cov[2]=agexact;
     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to                                          if(nagesqr==1)
        decrease memory allocation */                                                  cov[3]= agexact*agexact;
     for(theta=1; theta <=npar; theta++){                                          for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++){                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                                          }
         xm[i] = x[i] - (i==theta ?delti[theta]:0);                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);                                            savm=oldm;
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);                                            oldm=newm;
                                    } /* end mult */
       for(j=1; j<= nlstate; j++){        
         for(i=1; i<=nlstate; i++){                                  s1=s[mw[mi][i]][i];
           for(h=0; h<=nhstepm-1; h++){                                  s2=s[mw[mi+1][i]][i];
             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;                                  bbh=(double)bh[mi][i]/(double)stepm; 
             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;                                  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           }                                  ipmx +=1;
         }                                  sw += weight[i];
       }                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                                } /* end of wave */
       for(ij=1; ij<= nlstate*nlstate; ij++)                  } /* end of individual */
         for(h=0; h<=nhstepm-1; h++){          }  else if(mle==3){  /* exponential inter-extrapolation */
           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     }/* End theta */                          for(mi=1; mi<= wav[i]-1; mi++){
                                      for (ii=1;ii<=nlstate+ndeath;ii++)
                                              for (j=1;j<=nlstate+ndeath;j++){
     for(h=0; h<=nhstepm-1; h++)                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate*nlstate;j++)                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(theta=1; theta <=npar; theta++)                                          }
           trgradg[h][j][theta]=gradg[h][theta][j];                                  for(d=0; d<dh[mi][i]; d++){
                                              newm=savm;
                                           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
      for(ij=1;ij<=nlstate*nlstate;ij++)                                          cov[2]=agexact;
       for(ji=1;ji<=nlstate*nlstate;ji++)                                          if(nagesqr==1)
         varhe[ij][ji][(int)age] =0.;                                                  cov[3]= agexact*agexact;
                                           for (kk=1; kk<=cptcovage;kk++) {
      printf("%d|",(int)age);fflush(stdout);                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);                                          }
      for(h=0;h<=nhstepm-1;h++){                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(k=0;k<=nhstepm-1;k++){                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);                                          savm=oldm;
         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);                                          oldm=newm;
         for(ij=1;ij<=nlstate*nlstate;ij++)                                  } /* end mult */
           for(ji=1;ji<=nlstate*nlstate;ji++)        
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;                                  s1=s[mw[mi][i]][i];
       }                                  s2=s[mw[mi+1][i]][i];
     }                                  bbh=(double)bh[mi][i]/(double)stepm; 
                                   lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     /* Computing expectancies */                                  ipmx +=1;
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);                                    sw += weight[i];
     for(i=1; i<=nlstate;i++)                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<=nlstate;j++)                          } /* end of wave */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                  } /* end of individual */
           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;          }else if (mle==4){  /* ml=4 no inter-extrapolation */
                            for (i=1,ipmx=0, sw=0.; i<=imx; 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]);*/                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                           for(mi=1; mi<= wav[i]-1; mi++){
         }                                  for (ii=1;ii<=nlstate+ndeath;ii++)
                                           for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresstdeij,"%3.0f",age );                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++){                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
       eip=0.;                                          }
       vip=0.;                                  for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<=nlstate;j++){                                          newm=savm;
         eip += eij[i][j][(int)age];                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */                                          cov[2]=agexact;
           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];                                          if(nagesqr==1)
         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );                                                  cov[3]= agexact*agexact;
       }                                          for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     }                                          }
     fprintf(ficresstdeij,"\n");          
                                           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficrescveij,"%3.0f",age );                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)                                          savm=oldm;
       for(j=1; j<=nlstate;j++){                                          oldm=newm;
         cptj= (j-1)*nlstate+i;                                  } /* end mult */
         for(i2=1; i2<=nlstate;i2++)        
           for(j2=1; j2<=nlstate;j2++){                                  s1=s[mw[mi][i]][i];
             cptj2= (j2-1)*nlstate+i2;                                  s2=s[mw[mi+1][i]][i];
             if(cptj2 <= cptj)                                  if( s2 > nlstate){ 
               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);                                          lli=log(out[s1][s2] - savm[s1][s2]);
           }                                  } else if  ( s2==-1 ) { /* alive */
       }                                          for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficrescveij,"\n");                                                  survp += out[s1][j];
                                              lli= log(survp);
   }                                  }else{
   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);                                          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);                                  }
   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);                                  ipmx +=1;
   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);                                  sw += weight[i];
   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*      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("\n");                          } /* end of wave */
   fprintf(ficlog,"\n");                  } /* end of individual */
           }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   free_vector(xm,1,npar);                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(xp,1,npar);                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);                          for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);                                  for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);                                          for (j=1;j<=nlstate+ndeath;j++){
 }                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                                   savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Variance ******************/                                          }
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])                                  for(d=0; d<dh[mi][i]; d++){
 {                                          newm=savm;
   /* Variance of health expectancies */                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                                          cov[2]=agexact;
   /* double **newm;*/                                          if(nagesqr==1)
   double **dnewm,**doldm;                                                  cov[3]= agexact*agexact;
   double **dnewmp,**doldmp;                                          for (kk=1; kk<=cptcovage;kk++) {
   int i, j, nhstepm, hstepm, h, nstepm ;                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   int k, cptcode;                                          }
   double *xp;          
   double **gp, **gm;  /* for var eij */                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***gradg, ***trgradg; /*for var eij */                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **gradgp, **trgradgp; /* for var p point j */                                          savm=oldm;
   double *gpp, *gmp; /* for var p point j */                                          oldm=newm;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */                                  } /* end mult */
   double ***p3mat;        
   double age,agelim, hf;                                  s1=s[mw[mi][i]][i];
   double ***mobaverage;                                  s2=s[mw[mi+1][i]][i];
   int theta;                                  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   char digit[4];                                  ipmx +=1;
   char digitp[25];                                  sw += weight[i];
                                   ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresprobmorprev[FILENAMELENGTH];                                  /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
                           } /* end of wave */
   if(popbased==1){                  } /* end of individual */
     if(mobilav!=0)          } /* End of if */
       strcpy(digitp,"-populbased-mobilav-");          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     else strcpy(digitp,"-populbased-nomobil-");          /* 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 */
   else          return -l;
     strcpy(digitp,"-stablbased-");  }
   
   if (mobilav!=0) {  /*************** log-likelihood *************/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  double funcone( double *x)
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  {
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);    /* Same as likeli but slower because of a lot of printf and if */
       printf(" Error in movingaverage mobilav=%d\n",mobilav);    int i, ii, j, k, mi, d, kk;
     }          int ioffset=0;
   }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
   strcpy(fileresprobmorprev,"prmorprev");    double lli; /* Individual log likelihood */
   sprintf(digit,"%-d",ij);    double llt;
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    int s1, s2;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */    double bbh, survp;
   strcat(fileresprobmorprev,fileres);    double agexact;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    double agebegin, ageend;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    /*extern weight */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    */
   pstamp(ficresprobmorprev);    cov[1]=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(ficresprobmorprev,"# Age cov=%-d",ij);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    ioffset=0;
     fprintf(ficresprobmorprev," p.%-d SE",j);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1; i<=nlstate;i++)                  ioffset=2+nagesqr+cptcovage;
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
   }                    for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
   fprintf(ficresprobmorprev,"\n");                          cov[++ioffset]=covar[Tvar[k]][i];
   fprintf(ficgp,"\n# Routine varevsij");                  }
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/                  for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
   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");                          cov[++ioffset]=coqvar[iqv][i];
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);                  }
 /*   } */  
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for(mi=1; mi<= wav[i]-1; mi++){
   pstamp(ficresvij);                          for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");                                  cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
   if(popbased==1)                          }
     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");                          for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
   else                                  cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");                          }
   fprintf(ficresvij,"# Age");        for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=nlstate;i++)                                  for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<=nlstate;j++)                                          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);                                          savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvij,"\n");                                  }
         
   xp=vector(1,npar);        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
   dnewm=matrix(1,nlstate,1,npar);        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
   doldm=matrix(1,nlstate,1,nlstate);        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);                                  /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                                          and mw[mi+1][i]. dh depends on stepm.*/
                                   newm=savm;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);                                  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   gpp=vector(nlstate+1,nlstate+ndeath);                                  cov[2]=agexact;
   gmp=vector(nlstate+1,nlstate+ndeath);                                  if(nagesqr==1)
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/                                          cov[3]= agexact*agexact;
                                    for (kk=1; kk<=cptcovage;kk++) {
   if(estepm < stepm){                                          cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     printf ("Problem %d lower than %d\n",estepm, stepm);                                  }
   }                                  
   else  hstepm=estepm;                                    /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   /* For example we decided to compute the life expectancy with the smallest unit */                                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                                                                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      nhstepm is the number of hstepm from age to agelim                                  /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
      nstepm is the number of stepm from age to agelin.                                  /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
      Look at hpijx to understand the reason of that which relies in memory size                                  savm=oldm;
      and note for a fixed period like k years */                                  oldm=newm;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        } /* end mult */
      survival function given by stepm (the optimization length). Unfortunately it        
      means that if the survival funtion is printed every two years of age and if        s1=s[mw[mi][i]][i];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        s2=s[mw[mi+1][i]][i];
      results. So we changed our mind and took the option of the best precision.        /* if(s2==-1){ */
   */        /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        /*        /\* exit(1); *\/ */
   agelim = AGESUP;        /* } */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        bbh=(double)bh[mi][i]/(double)stepm; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /* bias is positive if real duration
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */         * is higher than the multiple of stepm and negative otherwise.
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     gp=matrix(0,nhstepm,1,nlstate);                                  lli=log(out[s1][s2] - savm[s1][s2]);
     gm=matrix(0,nhstepm,1,nlstate);        } else if  ( s2==-1 ) { /* alive */
                                   for (j=1,survp=0. ; j<=nlstate; j++) 
                                           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(theta=1; theta <=npar; theta++){                                  lli= log(survp);
       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/        }else if (mle==1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }        } else if(mle==2){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                                    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 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } else if(mle==3){  /* exponential inter-extrapolation */
                                   lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       if (popbased==1) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         if(mobilav ==0){                                  lli=log(out[s1][s2]); /* Original formula */
           for(i=1; i<=nlstate;i++)        } else{  /* mle=0 back to 1 */
             prlim[i][i]=probs[(int)age][i][ij];                                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }else{ /* mobilav */                                  /*lli=log(out[s1][s2]); */ /* Original formula */
           for(i=1; i<=nlstate;i++)        } /* End of if */
             prlim[i][i]=mobaverage[(int)age][i][ij];        ipmx +=1;
         }        sw += weight[i];
       }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(j=1; j<= nlstate; j++){        if(globpr){
         for(h=0; h<=nhstepm; h++){                                  fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)   %11.6f %11.6f %11.6f ", \
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                                                                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
         }                                                                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       }                                  for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       /* This for computing probability of death (h=1 means                                          llt +=ll[k]*gipmx/gsw;
          computed over hstepm matrices product = hstepm*stepm months)                                          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
          as a weighted average of prlim.                                  }
       */                                  fprintf(ficresilk," %10.6f\n", -llt);
       for(j=nlstate+1;j<=nlstate+ndeath;j++){        }
         for(i=1,gpp[j]=0.; i<= nlstate; i++)      } /* end of wave */
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    } /* end of individual */
       }        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       /* end probability of death */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */    if(globpr==0){ /* First time we count the contributions and weights */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      gipmx=ipmx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        gsw=sw;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
      return -l;
       if (popbased==1) {  }
         if(mobilav ==0){  
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][ij];  /*************** function likelione ***********/
         }else{ /* mobilav */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           for(i=1; i<=nlstate;i++)  {
             prlim[i][i]=mobaverage[(int)age][i][ij];    /* This routine should help understanding what is done with 
         }       the selection of individuals/waves and
       }       to check the exact contribution to the likelihood.
        Plotting could be done.
       for(j=1; j<= nlstate; j++){     */
         for(h=0; h<=nhstepm; h++){    int k;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    if(*globpri !=0){ /* Just counts and sums, no printings */
         }      strcpy(fileresilk,"ILK_"); 
       }      strcat(fileresilk,fileresu);
       /* This for computing probability of death (h=1 means      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          computed over hstepm matrices product = hstepm*stepm months)        printf("Problem with resultfile: %s\n", fileresilk);
          as a weighted average of prlim.        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       */      }
       for(j=nlstate+1;j<=nlstate+ndeath;j++){      fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
         for(i=1,gmp[j]=0.; i<= nlstate; i++)      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
          gmp[j] += prlim[i][i]*p3mat[i][j][1];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       }          for(k=1; k<=nlstate; k++) 
       /* end probability of death */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       for(j=1; j<= nlstate; j++) /* vareij */    }
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
       fclose(ficresilk);
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */      if (mle ==0)
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
       }      else if(mle >=1)
         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
     } /* End theta */      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));
       
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */        
       for (k=1; k<= nlstate ; k++) {
     for(h=0; h<=nhstepm; h++) /* veij */        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> \
       for(j=1; j<=nlstate;j++)  <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
         for(theta=1; theta <=npar; theta++)      }
           trgradg[h][j][theta]=gradg[h][theta][j];      fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
       for(theta=1; theta <=npar; theta++)  <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
         trgradgp[j][theta]=gradgp[theta][j];      fflush(fichtm);
      }
     return;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  /*********** Maximum Likelihood Estimation ***************/
   
     for(h=0;h<=nhstepm;h++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for(k=0;k<=nhstepm;k++){  {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int i,j, iter=0;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double **xi;
         for(i=1;i<=nlstate;i++)    double fret;
           for(j=1;j<=nlstate;j++)    double fretone; /* Only one call to likelihood */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    /*  char filerespow[FILENAMELENGTH];*/
       }  
     }  #ifdef NLOPT
      int creturn;
     /* pptj */    nlopt_opt opt;
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    double *lb;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    double minf; /* the minimum objective value, upon return */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    double * p1; /* Shifted parameters from 0 instead of 1 */
         varppt[j][i]=doldmp[j][i];    myfunc_data dinst, *d = &dinst;
     /* end ppptj */  #endif
     /*  x centered again */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);    
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
     if (popbased==1) {      for (j=1;j<=npar;j++)
       if(mobilav ==0){        xi[i][j]=(i==j ? 1.0 : 0.0);
         for(i=1; i<=nlstate;i++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           prlim[i][i]=probs[(int)age][i][ij];    strcpy(filerespow,"POW_"); 
       }else{ /* mobilav */    strcat(filerespow,fileres);
         for(i=1; i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           prlim[i][i]=mobaverage[(int)age][i][ij];      printf("Problem with resultfile: %s\n", filerespow);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }    }
                  fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /* This for computing probability of death (h=1 means    for (i=1;i<=nlstate;i++)
        computed over hstepm (estepm) matrices product = hstepm*stepm months)      for(j=1;j<=nlstate+ndeath;j++)
        as a weighted average of prlim.        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */    fprintf(ficrespow,"\n");
     for(j=nlstate+1;j<=nlstate+ndeath;j++){  #ifdef POWELL
       for(i=1,gmp[j]=0.;i<= nlstate; i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];  #endif
     }      
     /* end probability of death */  #ifdef NLOPT
   #ifdef NEWUOA
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){  #else
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
       for(i=1; i<=nlstate;i++){  #endif
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    lb=vector(0,npar-1);
       }    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     }    nlopt_set_lower_bounds(opt, lb);
     fprintf(ficresprobmorprev,"\n");    nlopt_set_initial_step1(opt, 0.1);
     
     fprintf(ficresvij,"%.0f ",age );    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     for(i=1; i<=nlstate;i++)    d->function = func;
       for(j=1; j<=nlstate;j++){    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    nlopt_set_min_objective(opt, myfunc, d);
       }    nlopt_set_xtol_rel(opt, ftol);
     fprintf(ficresvij,"\n");    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     free_matrix(gp,0,nhstepm,1,nlstate);      printf("nlopt failed! %d\n",creturn); 
     free_matrix(gm,0,nhstepm,1,nlstate);    }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    else {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   } /* End age */      iter=1; /* not equal */
   free_vector(gpp,nlstate+1,nlstate+ndeath);    }
   free_vector(gmp,nlstate+1,nlstate+ndeath);    nlopt_destroy(opt);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  #endif
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(xi,1,npar,1,npar);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    fclose(ficrespow);
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  }
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));  /**** Computes Hessian and covariance matrix ***/
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));  void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));  {
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    double  **a,**y,*x,pd;
   /*  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);    /* double **hess; */
 */    int i, j;
 /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */    int *indx;
   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   free_vector(xp,1,npar);    double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
   free_matrix(doldm,1,nlstate,1,nlstate);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   free_matrix(dnewm,1,nlstate,1,npar);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double gompertz(double p[]);
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    /* hess=matrix(1,npar,1,npar); */
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("\nCalculation of the hessian matrix. Wait...\n");
   fclose(ficresprobmorprev);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   fflush(ficgp);    for (i=1;i<=npar;i++){
   fflush(fichtm);      printf("%d-",i);fflush(stdout);
 }  /* end varevsij */      fprintf(ficlog,"%d-",i);fflush(ficlog);
      
 /************ Variance of prevlim ******************/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 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[])      
 {      /*  printf(" %f ",p[i]);
   /* Variance of prevalence limit */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    }
   double **newm;    
   double **dnewm,**doldm;    for (i=1;i<=npar;i++) {
   int i, j, nhstepm, hstepm;      for (j=1;j<=npar;j++)  {
   int k, cptcode;        if (j>i) { 
   double *xp;          printf(".%d-%d",i,j);fflush(stdout);
   double *gp, *gm;          fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
   double **gradg, **trgradg;          hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
   double age,agelim;          
   int theta;          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   pstamp(ficresvpl);        }
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");      }
   fprintf(ficresvpl,"# Age");    }
   for(i=1; i<=nlstate;i++)    printf("\n");
       fprintf(ficresvpl," %1d-%1d",i,i);    fprintf(ficlog,"\n");
   fprintf(ficresvpl,"\n");  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   xp=vector(1,npar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   hstepm=1*YEARM; /* Every year of age */    x=vector(1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    indx=ivector(1,npar);
   agelim = AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    ludcmp(a,npar,indx,&pd);
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (j=1;j<=npar;j++) {
     gradg=matrix(1,npar,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
     gp=vector(1,nlstate);      x[j]=1;
     gm=vector(1,nlstate);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     for(theta=1; theta <=npar; theta++){        matcov[i][j]=x[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    printf("\n#Hessian matrix#\n");
       for(i=1;i<=nlstate;i++)    fprintf(ficlog,"\n#Hessian matrix#\n");
         gp[i] = prlim[i][i];    for (i=1;i<=npar;i++) { 
          for (j=1;j<=npar;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */        printf("%.6e ",hess[i][j]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficlog,"%.6e ",hess[i][j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
       for(i=1;i<=nlstate;i++)      printf("\n");
         gm[i] = prlim[i][i];      fprintf(ficlog,"\n");
     }
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /* printf("\n#Covariance matrix#\n"); */
     } /* End theta */    /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
     /* for (i=1;i<=npar;i++) {  */
     trgradg =matrix(1,nlstate,1,npar);    /*   for (j=1;j<=npar;j++) {  */
     /*     printf("%.6e ",matcov[i][j]); */
     for(j=1; j<=nlstate;j++)    /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
       for(theta=1; theta <=npar; theta++)    /*   } */
         trgradg[j][theta]=gradg[theta][j];    /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     for(i=1;i<=nlstate;i++)    /* } */
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /* Recompute Inverse */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /* for (i=1;i<=npar;i++) */
     for(i=1;i<=nlstate;i++)    /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* ludcmp(a,npar,indx,&pd); */
   
     fprintf(ficresvpl,"%.0f ",age );    /*  printf("\n#Hessian matrix recomputed#\n"); */
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /* for (j=1;j<=npar;j++) { */
     fprintf(ficresvpl,"\n");    /*   for (i=1;i<=npar;i++) x[i]=0; */
     free_vector(gp,1,nlstate);    /*   x[j]=1; */
     free_vector(gm,1,nlstate);    /*   lubksb(a,npar,indx,x); */
     free_matrix(gradg,1,npar,1,nlstate);    /*   for (i=1;i<=npar;i++){  */
     free_matrix(trgradg,1,nlstate,1,npar);    /*     y[i][j]=x[i]; */
   } /* End age */    /*     printf("%.3e ",y[i][j]); */
     /*     fprintf(ficlog,"%.3e ",y[i][j]); */
   free_vector(xp,1,npar);    /*   } */
   free_matrix(doldm,1,nlstate,1,npar);    /*   printf("\n"); */
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*   fprintf(ficlog,"\n"); */
     /* } */
 }  
     /* Verifying the inverse matrix */
 /************ Variance of one-step probabilities  ******************/  #ifdef DEBUGHESS
 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[])    y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
 {  
   int i, j=0,  i1, k1, l1, t, tj;     printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
   int k2, l2, j1,  z1;     fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
   int k=0,l, cptcode;  
   int first=1, first1;    for (j=1;j<=npar;j++) {
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;      for (i=1;i<=npar;i++){ 
   double **dnewm,**doldm;        printf("%.2f ",y[i][j]);
   double *xp;        fprintf(ficlog,"%.2f ",y[i][j]);
   double *gp, *gm;      }
   double **gradg, **trgradg;      printf("\n");
   double **mu;      fprintf(ficlog,"\n");
   double age,agelim, cov[NCOVMAX];    }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  #endif
   int theta;  
   char fileresprob[FILENAMELENGTH];    free_matrix(a,1,npar,1,npar);
   char fileresprobcov[FILENAMELENGTH];    free_matrix(y,1,npar,1,npar);
   char fileresprobcor[FILENAMELENGTH];    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   double ***varpij;    /* free_matrix(hess,1,npar,1,npar); */
   
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);  }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  /*************** hessian matrix ****************/
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   }  { /* Around values of x, computes the function func and returns the scales delti and hessian */
   strcpy(fileresprobcov,"probcov");    int i;
   strcat(fileresprobcov,fileres);    int l=1, lmax=20;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    double k1,k2, res, fx;
     printf("Problem with resultfile: %s\n", fileresprobcov);    double p2[MAXPARM+1]; /* identical to x */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   }    int k=0,kmax=10;
   strcpy(fileresprobcor,"probcor");    double l1;
   strcat(fileresprobcor,fileres);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    fx=func(x);
     printf("Problem with resultfile: %s\n", fileresprobcor);    for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   }      l1=pow(10,l);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      delts=delt;
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      for(k=1 ; k <kmax; k=k+1){
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        delt = delta*(l1*k);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        p2[theta]=x[theta] +delt;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        p2[theta]=x[theta]-delt;
   pstamp(ficresprob);        k2=func(p2)-fx;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
   fprintf(ficresprob,"# Age");        res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
   pstamp(ficresprobcov);        
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  #ifdef DEBUGHESSII
   fprintf(ficresprobcov,"# Age");        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);
   pstamp(ficresprobcor);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  #endif
   fprintf(ficresprobcor,"# Age");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=(nlstate+ndeath);j++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          k=kmax; l=lmax*10;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     }            delts=delt;
  /* fprintf(ficresprob,"\n");        }
   fprintf(ficresprobcov,"\n");      } /* End loop k */
   fprintf(ficresprobcor,"\n");    }
  */    delti[theta]=delts;
  xp=vector(1,npar);    return res; 
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  }
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   first=1;  {
   fprintf(ficgp,"\n# Routine varprob");    int i;
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    int l=1, lmax=20;
   fprintf(fichtm,"\n");    double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);    int k, kmax=1;
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\    double v1, v2, cv12, lc1, lc2;
   file %s<br>\n",optionfilehtmcov);  
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\    int firstime=0;
 and drawn. It helps understanding how is the covariance between two incidences.\    
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    fx=func(x);
   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. \    for (k=1; k<=kmax; k=k+10) {
 It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \      for (i=1;i<=npar;i++) p2[i]=x[i];
 would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \      p2[thetai]=x[thetai]+delti[thetai]*k;
 standard deviations wide on each axis. <br>\      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\      k1=func(p2)-fx;
  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");      p2[thetai]=x[thetai]+delti[thetai]*k;
       p2[thetaj]=x[thetaj]-delti[thetaj]*k;
   cov[1]=1;      k2=func(p2)-fx;
   tj=cptcoveff;    
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      p2[thetai]=x[thetai]-delti[thetai]*k;
   j1=0;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
   for(t=1; t<=tj;t++){      k3=func(p2)-fx;
     for(i1=1; i1<=ncodemax[t];i1++){    
       j1++;      p2[thetai]=x[thetai]-delti[thetai]*k;
       if  (cptcovn>0) {      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
         fprintf(ficresprob, "\n#********** Variable ");      k4=func(p2)-fx;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
         fprintf(ficresprob, "**********\n#\n");      if(k1*k2*k3*k4 <0.){
         fprintf(ficresprobcov, "\n#********** Variable ");        firstime=1;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        kmax=kmax+10;
         fprintf(ficresprobcov, "**********\n#\n");      }
              if(kmax >=10 || firstime ==1){
         fprintf(ficgp, "\n#********** Variable ");        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);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        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);
         fprintf(ficgp, "**********\n#\n");        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
              }
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");  #ifdef DEBUGHESSIJ
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      v1=hess[thetai][thetai];
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");      v2=hess[thetaj][thetaj];
              cv12=res;
         fprintf(ficresprobcor, "\n#********** Variable ");          /* Computing eigen value of Hessian matrix */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         fprintf(ficresprobcor, "**********\n#");          lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       }      if ((lc2 <0) || (lc1 <0) ){
              printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
       for (age=bage; age<=fage; age ++){        fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         cov[2]=age;        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for (k=1; k<=cptcovn;k++) {        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      }
         }  #endif
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
         for (k=1; k<=cptcovprod;k++)    return res;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      /* Not done yet: Was supposed to fix if not exactly at the maximum */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
         gp=vector(1,(nlstate)*(nlstate+ndeath));  /* { */
         gm=vector(1,(nlstate)*(nlstate+ndeath));  /*   int i; */
      /*   int l=1, lmax=20; */
         for(theta=1; theta <=npar; theta++){  /*   double k1,k2,k3,k4,res,fx; */
           for(i=1; i<=npar; i++)  /*   double p2[MAXPARM+1]; */
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);  /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
            /*   int k=0,kmax=10; */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /*   double l1; */
              
           k=0;  /*   fx=func(x); */
           for(i=1; i<= (nlstate); i++){  /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
             for(j=1; j<=(nlstate+ndeath);j++){  /*     l1=pow(10,l); */
               k=k+1;  /*     delts=delt; */
               gp[k]=pmmij[i][j];  /*     for(k=1 ; k <kmax; k=k+1){ */
             }  /*       delt = delti*(l1*k); */
           }  /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
            /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
           for(i=1; i<=npar; i++)  /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);  /*       k1=func(p2)-fx; */
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
           k=0;  /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
           for(i=1; i<=(nlstate); i++){  /*       k2=func(p2)-fx; */
             for(j=1; j<=(nlstate+ndeath);j++){        
               k=k+1;  /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
               gm[k]=pmmij[i][j];  /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
             }  /*       k3=func(p2)-fx; */
           }        
        /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)  /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];    /*       k4=func(p2)-fx; */
         }  /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
   /* #ifdef DEBUGHESSIJ */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  /*       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(theta=1; theta <=npar; theta++)  /*       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); */
             trgradg[j][theta]=gradg[theta][j];  /* #endif */
          /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  /*      k=kmax; */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  /*       } */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  /*      k=kmax; l=lmax*10; */
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /*       } */
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
   /*      delts=delt; */
         pmij(pmmij,cov,ncovmodel,x,nlstate);  /*       } */
          /*     } /\* End loop k *\/ */
         k=0;  /*   } */
         for(i=1; i<=(nlstate); i++){  /*   delti[theta]=delts; */
           for(j=1; j<=(nlstate+ndeath);j++){  /*   return res;  */
             k=k+1;  /* } */
             mu[k][(int) age]=pmmij[i][j];  
           }  
         }  /************** Inverse of matrix **************/
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  void ludcmp(double **a, int n, int *indx, double *d) 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  { 
             varpij[i][j][(int)age] = doldm[i][j];    int i,imax,j,k; 
     double big,dum,sum,temp; 
         /*printf("\n%d ",(int)age);    double *vv; 
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){   
           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    vv=vector(1,n); 
           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    *d=1.0; 
           }*/    for (i=1;i<=n;i++) { 
       big=0.0; 
         fprintf(ficresprob,"\n%d ",(int)age);      for (j=1;j<=n;j++) 
         fprintf(ficresprobcov,"\n%d ",(int)age);        if ((temp=fabs(a[i][j])) > big) big=temp; 
         fprintf(ficresprobcor,"\n%d ",(int)age);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
         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 (j=1;j<=n;j++) { 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      for (i=1;i<j;i++) { 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        sum=a[i][j]; 
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
         i=0;      } 
         for (k=1; k<=(nlstate);k++){      big=0.0; 
           for (l=1; l<=(nlstate+ndeath);l++){      for (i=j;i<=n;i++) { 
             i=i++;        sum=a[i][j]; 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        for (k=1;k<j;k++) 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);          sum -= a[i][k]*a[k][j]; 
             for (j=1; j<=i;j++){        a[i][j]=sum; 
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          big=dum; 
             }          imax=i; 
           }        } 
         }/* end of loop for state */      } 
       } /* end of loop for age */      if (j != imax) { 
         for (k=1;k<=n;k++) { 
       /* Confidence intervalle of pij  */          dum=a[imax][k]; 
       /*          a[imax][k]=a[j][k]; 
         fprintf(ficgp,"\nset noparametric;unset label");          a[j][k]=dum; 
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");        } 
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        *d = -(*d); 
         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);        vv[imax]=vv[j]; 
         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      } 
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      indx[j]=imax; 
         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       */      if (j != n) { 
         dum=1.0/(a[j][j]); 
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       first1=1;      } 
       for (k2=1; k2<=(nlstate);k2++){    } 
         for (l2=1; l2<=(nlstate+ndeath);l2++){    free_vector(vv,1,n);  /* Doesn't work */
           if(l2==k2) continue;  ;
           j=(k2-1)*(nlstate+ndeath)+l2;  } 
           for (k1=1; k1<=(nlstate);k1++){  
             for (l1=1; l1<=(nlstate+ndeath);l1++){  void lubksb(double **a, int n, int *indx, double b[]) 
               if(l1==k1) continue;  { 
               i=(k1-1)*(nlstate+ndeath)+l1;    int i,ii=0,ip,j; 
               if(i<=j) continue;    double sum; 
               for (age=bage; age<=fage; age ++){   
                 if ((int)age %5==0){    for (i=1;i<=n;i++) { 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      ip=indx[i]; 
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      sum=b[ip]; 
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      b[ip]=b[i]; 
                   mu1=mu[i][(int) age]/stepm*YEARM ;      if (ii) 
                   mu2=mu[j][(int) age]/stepm*YEARM;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   c12=cv12/sqrt(v1*v2);      else if (sum) ii=i; 
                   /* Computing eigen value of matrix of covariance */      b[i]=sum; 
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    } 
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    for (i=n;i>=1;i--) { 
                   /* Eigen vectors */      sum=b[i]; 
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   /*v21=sqrt(1.-v11*v11); *//* error */      b[i]=sum/a[i][i]; 
                   v21=(lc1-v1)/cv12*v11;    } 
                   v12=-v21;  } 
                   v22=v11;  
                   tnalp=v21/v11;  void pstamp(FILE *fichier)
                   if(first1==1){  {
                     first1=0;    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);  }
                   }  
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);  /************ Frequencies ********************/
                   /*printf(fignu*/   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                                                                           int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],  \
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                                                                           int firstpass,  int lastpass, int stepm, int weightopt, char model[])
                   if(first==1){   {  /* Some frequencies */
                     first=0;    
                     fprintf(ficgp,"\nset parametric;unset label");           int i, m, jk, j1, bool, z1,j;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);           int iind=0, iage=0;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");           int mi; /* Effective wave */
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\           int first;
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\           double ***freq; /* Frequencies */
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\           double *meanq;
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\           double **meanqt;
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);           double *pp, **prop, *posprop, *pospropt;
                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);           double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);           char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);           double agebegin, ageend;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);      
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);           pp=vector(1,nlstate);
                     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",\           prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\           posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));           pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
                   }else{           /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
                     first=0;           meanq=vector(1,nqveff);
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);           meanqt=matrix(1,lastpass,1,nqtveff);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);           strcpy(fileresp,"P_");
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);           strcat(fileresp,fileresu);
                     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",\           /*strcat(fileresphtm,fileresu);*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\           if((ficresp=fopen(fileresp,"w"))==NULL) {
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                   printf("Problem with prevalence resultfile: %s\n", fileresp);
                   }/* if first */                   fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                 } /* age mod 5 */                   exit(0);
               } /* end loop age */           }
               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);  
               first=1;           strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
             } /*l12 */           if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
           } /* k12 */                   printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
         } /*l1 */                   fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       }/* k1 */                   fflush(ficlog);
     } /* loop covariates */                   exit(70); 
   }           }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);           else{
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);                   fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  <hr size=\"2\" color=\"#EC5E5E\"> \n\
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
   free_vector(xp,1,npar);                                                   fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   fclose(ficresprob);           }
   fclose(ficresprobcov);           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);
   fclose(ficresprobcor);      
   fflush(ficgp);           strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
   fflush(fichtmcov);           if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
 }                   printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                    fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                    fflush(ficlog);
 /******************* Printing html file ***********/                   exit(70); 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \           }
                   int lastpass, int stepm, int weightopt, char model[],\           else{
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                   fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   int popforecast, int estepm ,\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   double jprev1, double mprev1,double anprev1, \  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
                   double jprev2, double mprev2,double anprev2){                                                   fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   int jj1, k1, i1, cpt;           }
            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);
    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 \           freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
 </ul>");           j1=0;
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \    
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",           j=ncoveff;
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));           if (cptcovn<1) {j=1;ncodemax[1]=1;}
    fprintf(fichtm,"\  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",           first=1;
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));  
    fprintf(fichtm,"\           /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",                          reference=low_education V1=0,V2=0
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));                          med_educ                V1=1 V2=0, 
    fprintf(fichtm,"\                          high_educ               V1=0 V2=1
  - (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): \                          Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
    <a href=\"%s\">%s</a> <br>\n",           */
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));  
    fprintf(fichtm,"\           for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */
  - Population projections by age and states: \                   posproptt=0.;
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));                   /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                            scanf("%d", i);*/
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");                   for (i=-5; i<=nlstate+ndeath; i++)  
                            for (jk=-5; jk<=nlstate+ndeath; jk++)  
  m=cptcoveff;                                   for(m=iagemin; m <= iagemax+3; m++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                                           freq[i][jk][m]=0;
         
  jj1=0;                   for (i=1; i<=nlstate; i++)  {
  for(k1=1; k1<=m;k1++){                           for(m=iagemin; m <= iagemax+3; m++)
    for(i1=1; i1<=ncodemax[k1];i1++){                                   prop[i][m]=0;
      jj1++;                           posprop[i]=0;
      if (cptcovn > 0) {                           pospropt[i]=0;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                   }
        for (cpt=1; cpt<=cptcoveff;cpt++)                   for (z1=1; z1<= nqveff; z1++) {  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                           meanq[z1]+=0.;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                           for(m=1;m<=lastpass;m++){
      }                                   meanqt[m][z1]=0.;
      /* Pij */                           }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%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);            
      /* Quasi-incidences */                   dateintsum=0;
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\                   k2cpt=0;
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \       /* For that comination of covariate j1, we count and print the frequencies */
 <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);                   for (iind=1; iind<=imx; iind++) { /* For each individual iind */
        /* Period (stable) prevalence in each health state */                           bool=1;
        for(cpt=1; cpt<nlstate;cpt++){                           if (nqveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \                                   for (z1=1; z1<= nqveff; z1++) {  
 <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);                                           meanq[z1]+=coqvar[Tvar[z1]][iind];
        }                                   }
      for(cpt=1; cpt<=nlstate;cpt++) {                                   for (z1=1; z1<=ncoveff; z1++) {  
         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(Tvaraff[z1] ==-20){ */
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);                                           /*      /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
      }                                           /* }else  if(Tvaraff[z1] ==-10){ */
    } /* end i1 */                                           /*      /\* sumnew+=coqvar[z1][iind]; *\/ */
  }/* End k1 */                                           /* }else  */
  fprintf(fichtm,"</ul>");                                           if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                                                    /* Tests if this individual i responded to j1 (V4=1 V3=0) */
                                                    bool=0;
  fprintf(fichtm,"\                                                   /* 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", 
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                                                    /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",                                           } 
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));                                   } /* end z1 */
  fprintf(fichtm,"\                           } /* cptcovn > 0 */
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",  
          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));                           if (bool==1){ /* We selected an individual iin satisfying combination j1 */
                                    /* for(m=firstpass; m<=lastpass; m++){ */
  fprintf(fichtm,"\                                   for(mi=1; mi<wav[iind];mi++){
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",                                           m=mw[mi][iind];
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));                                           /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
  fprintf(fichtm,"\                                                          and mw[mi+1][iind]. dh depends on stepm. */
  - 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): \                                           agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
    <a href=\"%s\">%s</a> <br>\n</li>",                                           ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));                                           if(m >=firstpass && m <=lastpass){
  fprintf(fichtm,"\                                                   k2=anint[m][iind]+(mint[m][iind]/12.);
  - (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): \                                                   /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
    <a href=\"%s\">%s</a> <br>\n</li>",                                                   if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));                                                   if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
  fprintf(fichtm,"\                                                   if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
  - 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",                                                           prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));                                                   if (m<lastpass) {
  fprintf(fichtm,"\                                                           /* if(s[m][iind]==4 && s[m+1][iind]==4) */
  - 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",                                                           /*   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]); */
          subdirf2(fileres,"t"),subdirf2(fileres,"t"));                                                           if(s[m][iind]==-1)
  fprintf(fichtm,"\                                                                   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.));
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\                                                           freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));                                                           /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                                                            freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
 /*  if(popforecast==1) 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 */                                           if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
 /*      <br>",fileres,fileres,fileres,fileres); */                                                   dateintsum=dateintsum+k2;
 /*  else  */                                                   k2cpt++;
 /*    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); */                                                   /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
  fflush(fichtm);                                           }
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");                                           /*}*/
                                    } /* end m */
  m=cptcoveff;                           } /* end bool */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                   } /* end iind = 1 to imx */
          /* prop[s][age] is feeded for any initial and valid live state as well as
  jj1=0;                                          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;                   /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      if (cptcovn > 0) {                   pstamp(ficresp);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                   if  (ncoveff>0) {
        for (cpt=1; cpt<=cptcoveff;cpt++)                           fprintf(ficresp, "\n#********** Variable "); 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
      }                           for (z1=1; z1<=ncoveff; z1++){
      for(cpt=1; cpt<=nlstate;cpt++) {                                   fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \                                   fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\                                   fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);                             }
      }                           fprintf(ficresp, "**********\n#");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \                           fprintf(ficresphtm, "**********</h3>\n");
 health expectancies in states (1) and (2): %s%d.png<br>\                           fprintf(ficresphtmfr, "**********</h3>\n");
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);                           fprintf(ficlog, "\n#********** Variable "); 
    } /* end i1 */                           for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
  }/* End k1 */                           fprintf(ficlog, "**********\n");
  fprintf(fichtm,"</ul>");                   }
  fflush(fichtm);                   fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
 }                   for(i=1; i<=nlstate;i++) {
                            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 /******************* Gnuplot file **************/                           fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                   }
                    fprintf(ficresp, "\n");
   char dirfileres[132],optfileres[132];                   fprintf(ficresphtm, "\n");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        
   int ng;                   /* Header of frequency table by age */
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */                   fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
 /*     printf("Problem with file %s",optionfilegnuplot); */                   fprintf(ficresphtmfr,"<th>Age</th> ");
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */                   for(jk=-1; jk <=nlstate+ndeath; jk++){
 /*   } */                           for(m=-1; m <=nlstate+ndeath; m++){
                                    if(jk!=0 && m!=0)
   /*#ifdef windows */                                           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
   fprintf(ficgp,"cd \"%s\" \n",pathc);                           }
     /*#endif */                   }
   m=pow(2,cptcoveff);                   fprintf(ficresphtmfr, "\n");
         
   strcpy(dirfileres,optionfilefiname);                   /* For each age */
   strcpy(optfileres,"vpl");                   for(iage=iagemin; iage <= iagemax+3; iage++){
  /* 1eme*/                           fprintf(ficresphtm,"<tr>");
   for (cpt=1; cpt<= nlstate ; cpt ++) {                           if(iage==iagemax+1){
    for (k1=1; k1<= m ; k1 ++) {                                   fprintf(ficlog,"1");
      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);                                   fprintf(ficresphtmfr,"<tr><th>0</th> ");
      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);                           }else if(iage==iagemax+2){
      fprintf(ficgp,"set xlabel \"Age\" \n\                                   fprintf(ficlog,"0");
 set ylabel \"Probability\" \n\                                   fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
 set ter png small\n\                           }else if(iage==iagemax+3){
 set size 0.65,0.65\n\                                   fprintf(ficlog,"Total");
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);                                   fprintf(ficresphtmfr,"<tr><th>Total</th> ");
                            }else{
      for (i=1; i<= nlstate ; i ++) {                                   if(first==1){
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                                           first=0;
        else fprintf(ficgp," \%%*lf (\%%*lf)");                                           printf("See log file for details...\n");
      }                                   }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);                                   fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
      for (i=1; i<= nlstate ; i ++) {                                   fprintf(ficlog,"Age %d", iage);
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                           }
        else fprintf(ficgp," \%%*lf (\%%*lf)");                           for(jk=1; jk <=nlstate ; jk++){
      }                                   for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);                                           pp[jk] += freq[jk][m][iage]; 
      for (i=1; i<= nlstate ; i ++) {                           }
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                           for(jk=1; jk <=nlstate ; jk++){
        else fprintf(ficgp," \%%*lf (\%%*lf)");                                   for(m=-1, pos=0; m <=0 ; m++)
      }                                             pos += freq[jk][m][iage];
      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));                                   if(pp[jk]>=1.e-10){
    }                                           if(first==1){
   }                                                   printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /*2 eme*/                                           }
                                             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   for (k1=1; k1<= m ; k1 ++) {                                   }else{
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);                                           if(first==1)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);                                                   printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                                               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for (i=1; i<= nlstate+1 ; i ++) {                                   }
       k=2*i;                           }
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {                           for(jk=1; jk <=nlstate ; jk++){ 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                                   /* posprop[jk]=0; */
         else fprintf(ficgp," \%%*lf (\%%*lf)");                                   for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
       }                                             pp[jk] += freq[jk][m][iage];
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                           }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);                           for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
       for (j=1; j<= nlstate+1 ; j ++) {                                   pos += pp[jk]; /* pos is the total number of transitions until this age */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                                   posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
         else fprintf(ficgp," \%%*lf (\%%*lf)");                                                                                                                                                                           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
       fprintf(ficgp,"\" t\"\" w l 0,");                                                                                                                                                                           from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);                           }
       for (j=1; j<= nlstate+1 ; j ++) {                           for(jk=1; jk <=nlstate ; jk++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                                   if(pos>=1.e-5){
         else fprintf(ficgp," \%%*lf (\%%*lf)");                                           if(first==1)
       }                                                     printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                                           fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       else fprintf(ficgp,"\" t\"\" w l 0,");                                   }else{
     }                                           if(first==1)
   }                                                   printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                                             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /*3eme*/                                   }
                                     if( iage <= iagemax){
   for (k1=1; k1<= m ; k1 ++) {                                           if(pos>=1.e-5){
     for (cpt=1; cpt<= nlstate ; cpt ++) {                                                   fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
       /*       k=2+nlstate*(2*cpt-2); */                                                   fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
       k=2+(nlstate+1)*(cpt-1);                                                   /*probs[iage][jk][j1]= pp[jk]/pos;*/
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,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(ficgp,"set ter png small\n\                                           }
 set size 0.65,0.65\n\                                           else{
 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(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                                                   fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                                           }
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                                   }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                                   pospropt[jk] +=posprop[jk];
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                           } /* end loop jk */
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                           /* pospropt=0.; */
                                   for(jk=-1; jk <=nlstate+ndeath; jk++){
       */                                   for(m=-1; m <=nlstate+ndeath; m++){
       for (i=1; i< nlstate ; i ++) {                                           if(freq[jk][m][iage] !=0 ) { /* minimizing output */
         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);                                                   if(first==1){
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/                                                           printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                                                           }
       }                                                   fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);                                           }
     }                                           if(jk!=0 && m!=0)
   }                                                   fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
                                     }
   /* CV preval stable (period) */                           } /* end loop jk */
   for (k1=1; k1<= m ; k1 ++) {                           posproptt=0.; 
     for (cpt=1; cpt<=nlstate ; cpt ++) {                           for(jk=1; jk <=nlstate; jk++){
       k=3;                                   posproptt += pospropt[jk];
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);                           }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\                           fprintf(ficresphtmfr,"</tr>\n ");
 set ter png small\nset size 0.65,0.65\n\                           if(iage <= iagemax){
 unset log y\n\                                   fprintf(ficresp,"\n");
 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);                                   fprintf(ficresphtm,"</tr>\n");
                                 }
       for (i=1; i< nlstate ; i ++)                           if(first==1)
         fprintf(ficgp,"+$%d",k+i+1);                                   printf("Others in log...\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                           fprintf(ficlog,"\n");
                         } /* end loop age iage */
       l=3+(nlstate+ndeath)*cpt;                   fprintf(ficresphtm,"<tr><th>Tot</th>");
       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);                   for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i< nlstate ; i ++) {                           if(posproptt < 1.e-5){
         l=3+(nlstate+ndeath)*cpt;                                   fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);  
         fprintf(ficgp,"+$%d",l+i+1);                           }else{
       }                                   fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                             }
     }                   }
   }                     fprintf(ficresphtm,"</tr>\n");
                     fprintf(ficresphtm,"</table>\n");
   /* proba elementaires */                   fprintf(ficresphtmfr,"</table>\n");
   for(i=1,jk=1; i <=nlstate; i++){                   if(posproptt < 1.e-5){
     for(k=1; k <=(nlstate+ndeath); k++){                           fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
       if (k != i) {                           fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         for(j=1; j <=ncovmodel; j++){                           fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                           invalidvarcomb[j1]=1;
           jk++;                   }else{
           fprintf(ficgp,"\n");                           fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
         }                           invalidvarcomb[j1]=0;
       }                   }
     }                   fprintf(ficresphtmfr,"</table>\n");
    }           } /* end selected combination of covariate j1 */
            dateintmean=dateintsum/k2cpt; 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/                   
      for(jk=1; jk <=m; jk++) {           fclose(ficresp);
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);           fclose(ficresphtm);
        if (ng==2)           fclose(ficresphtmfr);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           free_vector(meanq,1,nqveff);
        else           free_matrix(meanqt,1,lastpass,1,nqtveff);
          fprintf(ficgp,"\nset title \"Probability\"\n");           free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);           free_vector(pospropt,1,nlstate);
        i=1;           free_vector(posprop,1,nlstate);
        for(k2=1; k2<=nlstate; k2++) {           free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
          k3=i;           free_vector(pp,1,nlstate);
          for(k=1; k<=(nlstate+ndeath); k++) {           /* End of freqsummary */
            if (k != k2){   }
              if(ng==2)  
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);  /************ Prevalence ********************/
              else   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);   {  
              ij=1;     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
              for(j=3; j <=ncovmodel; j++) {        in each health status at the date of interview (if between dateprev1 and dateprev2).
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        We still use firstpass and lastpass as another selection.
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);     */
                  ij++;   
                }     int i, m, jk, j1, bool, z1,j;
                else     int mi; /* Effective wave */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);     int iage;
              }     double agebegin, ageend;
              fprintf(ficgp,")/(1");  
                   double **prop;
              for(k1=1; k1 <=nlstate; k1++){       double posprop; 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);     double  y2; /* in fractional years */
                ij=1;     int iagemin, iagemax;
                for(j=3; j <=ncovmodel; j++){     int first; /** to stop verbosity which is redirected to log file */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);     iagemin= (int) agemin;
                    ij++;     iagemax= (int) agemax;
                  }     /*pp=vector(1,nlstate);*/
                  else     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                }     j1=0;
                fprintf(ficgp,")");    
              }     /*j=cptcoveff;*/
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);     if (cptcovn<1) {j=1;ncodemax[1]=1;}
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
              i=i+ncovmodel;     first=1;
            }     for(j1=1; j1<= (int) pow(2,nqveff);j1++){ /* For each combination of covariate */
          } /* end k */       for (i=1; i<=nlstate; i++)  
        } /* end k2 */         for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
      } /* end jk */           prop[i][iage]=0.0;
    } /* end ng */      
    fflush(ficgp);       for (i=1; i<=imx; i++) { /* Each individual */
 }  /* end gnuplot */         bool=1;
          if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
            for (z1=1; z1<=nqveff; 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*/
 /*************** Moving average **************/             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){               bool=0;
          } 
   int i, cpt, cptcod;         if (bool==1) { /* For this combination of covariates values, this individual fits */
   int modcovmax =1;           /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
   int mobilavrange, mob;           for(mi=1; mi<wav[i];mi++){
   double age;             m=mw[mi][i];
              agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                            a covariate has 2 modalities */             if(m >=firstpass && m <=lastpass){
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
     if(mobilav==1) mobilavrange=5; /* default */                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
     else mobilavrange=mobilav;                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
     for (age=bage; age<=fage; age++)                   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); 
       for (i=1; i<=nlstate;i++)                   exit(1);
         for (cptcod=1;cptcod<=modcovmax;cptcod++)                 }
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
     /* We keep the original values on the extreme ages bage, fage and for                   /*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]]);*/
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
        we use a 5 terms etc. until the borders are no more concerned.                   prop[s[m][i]][iagemax+3] += weight[i]; 
     */                 } /* end valid statuses */ 
     for (mob=3;mob <=mobilavrange;mob=mob+2){               } /* end selection of dates */
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){             } /* end selection of waves */
         for (i=1; i<=nlstate;i++){           } /* end effective waves */
           for (cptcod=1;cptcod<=modcovmax;cptcod++){         } /* end bool */
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];       }
               for (cpt=1;cpt<=(mob-1)/2;cpt++){       for(i=iagemin; i <= iagemax+3; i++){  
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];           posprop += prop[jk][i]; 
               }         } 
             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;        
           }         for(jk=1; jk <=nlstate ; jk++){      
         }           if( i <=  iagemax){ 
       }/* end age */             if(posprop>=1.e-5){ 
     }/* end mob */               probs[i][jk][j1]= prop[jk][i]/posprop;
   }else return -1;             } else{
   return 0;               if(first==1){
 }/* End movingaverage */                 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]);
                }
 /************** Forecasting ******************/             }
 prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){           } 
   /* proj1, year, month, day of starting projection         }/* end jk */ 
      agemin, agemax range of age       }/* end i */ 
      dateprev1 dateprev2 range of dates during which prevalence is computed       /*} *//* end i1 */
      anproj2 year of en of projection (same day and month as proj1).     } /* end j1 */
   */    
   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   int *popage;     /*free_vector(pp,1,nlstate);*/
   double agec; /* generic age */     free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   }  /* End of prevalence */
   double *popeffectif,*popcount;  
   double ***p3mat;  /************* Waves Concatenation ***************/
   double ***mobaverage;  
   char fileresf[FILENAMELENGTH];  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)
   {
   agelim=AGESUP;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);       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
   strcpy(fileresf,"f");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   strcat(fileresf,fileres);       and mw[mi+1][i]. dh depends on stepm.
   if((ficresf=fopen(fileresf,"w"))==NULL) {       */
     printf("Problem with forecast resultfile: %s\n", fileresf);  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    int i=0, mi=0, m=0, mli=0;
   }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);       double sum=0., jmean=0.;*/
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
     int j, k=0,jk, ju, jl;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double sum=0.;
     first=0;
   if (mobilav!=0) {    firstwo=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    firsthree=0;
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){    firstfour=0;
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);    jmin=100000;
       printf(" Error in movingaverage mobilav=%d\n",mobilav);    jmax=-1;
     }    jmean=0.;
   }  
   /* Treating live states */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
   if (stepm<=12) stepsize=1;      mi=0;  /* First valid wave */
   if(estepm < stepm){                  mli=0; /* Last valid wave */
     printf ("Problem %d lower than %d\n",estepm, stepm);      m=firstpass;
   }      while(s[m][i] <= nlstate){  /* a live state */
   else  hstepm=estepm;                            if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
                                   mli=m-1;/* mw[++mi][i]=m-1; */
   hstepm=hstepm/stepm;                          }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and                                  mw[++mi][i]=m;
                                fractional in yp1 */                                  mli=m;
   anprojmean=yp;        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
   yp2=modf((yp1*12),&yp);        if(m < lastpass){ /* m < lastpass, standard case */
   mprojmean=yp;                                  m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
   yp1=modf((yp2*30.5),&yp);        }
   jprojmean=yp;                          else{ /* m >= lastpass, eventual special issue with warning */
   if(jprojmean==0) jprojmean=1;  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
   if(mprojmean==0) jprojmean=1;                                  break;
   #else
   i1=cptcoveff;                                  if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
   if (cptcovn < 1){i1=1;}                                          if(firsthree == 0){
                                                    printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);                                                  firsthree=1;
                                            }
   fprintf(ficresf,"#****** Routine prevforecast **\n");                                          fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
                                           mw[++mi][i]=m;
 /*            if (h==(int)(YEARM*yearp)){ */                                          mli=m;
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){                                  }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                                  if(s[m][i]==-2){ /* Vital status is really unknown */
       k=k+1;                                          nbwarn++;
       fprintf(ficresf,"\n#******");                                          if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
       for(j=1;j<=cptcoveff;j++) {                                                  printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                                  fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
       }                                          }
       fprintf(ficresf,"******\n");                                          break;
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");                                  }
       for(j=1; j<=nlstate+ndeath;j++){                                  break;
         for(i=1; i<=nlstate;i++)                #endif
           fprintf(ficresf," p%d%d",i,j);                          }/* End m >= lastpass */
         fprintf(ficresf," p.%d",j);      }/* end while */
       }  
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {          /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
         fprintf(ficresf,"\n");      /* After last pass */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);    /* Treating death states */
       if (s[m][i] > nlstate){  /* In a death state */
         for (agec=fage; agec>=(ageminpar-1); agec--){                          /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);                          /* } */
           nhstepm = nhstepm/hstepm;        mi++;     /* Death is another wave */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* if(mi==0)  never been interviewed correctly before death */
           oldm=oldms;savm=savms;                          /* Only death is a correct wave */
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);          mw[mi][i]=m;
              }
           for (h=0; h<=nhstepm; h++){  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
             if (h*hstepm/YEARM*stepm ==yearp) {                  else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
               fprintf(ficresf,"\n");        /* m++; */
               for(j=1;j<=cptcoveff;j++)        /* mi++; */
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);        /* mw[mi][i]=m; */
             }        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
             for(j=1; j<=nlstate+ndeath;j++) {                                  if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
               ppij=0.;                                          nbwarn++;
               for(i=1; i<=nlstate;i++) {                                          if(firstfiv==0){
                 if (mobilav==1)                                                  printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];                                                  firstfiv=1;
                 else {                                          }else{
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];                                                  fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                 }                                          }
                 if (h*hstepm/YEARM*stepm== yearp) {                                  }else{ /* Death occured afer last wave potential bias */
                   fprintf(ficresf," %.3f", p3mat[i][j][h]);                                          nberr++;
                 }                                          if(firstwo==0){
               } /* end i */                                                  printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
               if (h*hstepm/YEARM*stepm==yearp) {                                                  firstwo=1;
                 fprintf(ficresf," %.3f", ppij);                                          }
               }                                          fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
             }/* end j */                                  }
           } /* end h */        }else{ /* end date of interview is known */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                  /* death is known but not confirmed by death status at any wave */
         } /* end agec */                                  if(firstfour==0){
       } /* end yearp */                                          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 );
     } /* end cptcod */                                          firstfour=1;
   } /* end  cptcov */                                  }
                                          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 );
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
       } /* end if date of death is known */
   fclose(ficresf);  #endif
 }      wav[i]=mi; /* mi should be the last effective wave (or mli) */
       /* wav[i]=mw[mi][i]; */
 /************** Forecasting *****not tested NB*************/      if(mi==0){
 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){        nbwarn++;
          if(first==0){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   int *popage;                                  first=1;
   double calagedatem, agelim, kk1, kk2;        }
   double *popeffectif,*popcount;        if(first==1){
   double ***p3mat,***tabpop,***tabpopprev;                                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   double ***mobaverage;        }
   char filerespop[FILENAMELENGTH];      } /* end mi==0 */
     } /* End individuals */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* wav and mw are no more changed */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
   agelim=AGESUP;    
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    for(i=1; i<=imx; i++){
        for(mi=1; mi<wav[i];mi++){
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);        if (stepm <=0)
                                    dh[mi][i]=1;
          else{
   strcpy(filerespop,"pop");                                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   strcat(filerespop,fileres);                                          if (agedc[i] < 2*AGESUP) {
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                                                  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     printf("Problem with forecast resultfile: %s\n", filerespop);                                                  if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);                                                  else if(j<0){
   }                                                          nberr++;
   printf("Computing forecasting: result on file '%s' \n", filerespop);                                                          printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);                                                          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);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                                                          fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                           fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   if (mobilav!=0) {                                                  }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                                                  k=k+1;
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){                                                  if (j >= jmax){
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);                                                          jmax=j;
       printf(" Error in movingaverage mobilav=%d\n",mobilav);                                                          ijmax=i;
     }                                                  }
   }                                                  if (j <= jmin){
                                                           jmin=j;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                                                          ijmin=i;
   if (stepm<=12) stepsize=1;                                                  }
                                                    sum=sum+j;
   agelim=AGESUP;                                                  /*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);*/
   hstepm=1;                                          }
   hstepm=hstepm/stepm;                                  }
                                    else{
   if (popforecast==1) {                                          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     if((ficpop=fopen(popfile,"r"))==NULL) {  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       printf("Problem with population file : %s\n",popfile);exit(0);                                          
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);                                          k=k+1;
     }                                          if (j >= jmax) {
     popage=ivector(0,AGESUP);                                                  jmax=j;
     popeffectif=vector(0,AGESUP);                                                  ijmax=i;
     popcount=vector(0,AGESUP);                                          }
                                              else if (j <= jmin){
     i=1;                                                    jmin=j;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                                                  ijmin=i;
                                              }
     imx=i;                                          /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                                          /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   }                                          if(j<0){
                                                   nberr++;
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){                                                  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]);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                                                  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]);
       k=k+1;                                          }
       fprintf(ficrespop,"\n#******");                                          sum=sum+j;
       for(j=1;j<=cptcoveff;j++) {                                  }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  jk= j/stepm;
       }                                  jl= j -jk*stepm;
       fprintf(ficrespop,"******\n");                                  ju= j -(jk+1)*stepm;
       fprintf(ficrespop,"# Age");                                  if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                                          if(jl==0){
       if (popforecast==1)  fprintf(ficrespop," [Population]");                                                  dh[mi][i]=jk;
                                                        bh[mi][i]=0;
       for (cpt=0; cpt<=0;cpt++) {                                          }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                                                                            * to avoid the price of an extra matrix product in likelihood */
                                                          dh[mi][i]=jk+1;
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){                                                  bh[mi][i]=ju;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                                          }
           nhstepm = nhstepm/hstepm;                                  }else{
                                                    if(jl <= -ju){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                                  dh[mi][i]=jk;
           oldm=oldms;savm=savms;                                                  bh[mi][i]=jl;   /* bias is positive if real duration
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                                                                                                             * is higher than the multiple of stepm and negative otherwise.
                                                                                                                   */
           for (h=0; h<=nhstepm; h++){                                          }
             if (h==(int) (calagedatem+YEARM*cpt)) {                                          else{
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                                                  dh[mi][i]=jk+1;
             }                                                  bh[mi][i]=ju;
             for(j=1; j<=nlstate+ndeath;j++) {                                          }
               kk1=0.;kk2=0;                                          if(dh[mi][i]==0){
               for(i=1; i<=nlstate;i++) {                                                                dh[mi][i]=1; /* At least one step */
                 if (mobilav==1)                                                  bh[mi][i]=ju; /* At least one step */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                                                  /*  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);*/
                 else {                                          }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                                  } /* end if mle */
                 }        }
               }      } /* end wave */
               if (h==(int)(calagedatem+12*cpt)){    }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    jmean=sum/k;
                   /*fprintf(ficrespop," %.3f", kk1);    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 (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+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);
               }   }
             }  
             for(i=1; i<=nlstate;i++){  /*********** Tricode ****************************/
               kk1=0.;   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
                 for(j=1; j<=nlstate;j++){  {
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
                 }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];     * Boring subroutine which should only output nbcode[Tvar[j]][k]
             }     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
      * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)    */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int modmaxcovj=0; /* Modality max of covariates j */
         }    int cptcode=0; /* Modality max of covariates j */
       }    int modmincovj=0; /* Modality min of covariates j */
    
   /******/  
     /* cptcoveff=0;  */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          /* *cptcov=0; */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    /* Loop on covariates without age and products and no quantitative variable */
              /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (j=1; j<=(*cptcov); j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
           oldm=oldms;savm=savms;      for (k=-1; k < maxncov; k++) Ndum[k]=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
           for (h=0; h<=nhstepm; h++){                                                                                                                                  modality of this covariate Vj*/
             if (h==(int) (calagedatem+YEARM*cpt)) {                          if(Tvar[j]  >=1 && Tvar[j]  <= *cptcov){ /* A real fixed covariate */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                                  ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
             }                                                                                                                                                          * If product of Vn*Vm, still boolean *:
             for(j=1; j<=nlstate+ndeath;j++) {                                                                                                                                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
               kk1=0.;kk2=0;                                                                                                                                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
               for(i=1; i<=nlstate;i++) {                                                /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                                               modality of the nth covariate of individual i. */
               }                                  if (ij > modmaxcovj)
               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);                                                  modmaxcovj=ij; 
             }                                  else if (ij < modmincovj) 
           }                                          modmincovj=ij; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                  if ((ij < -1) && (ij > NCOVMAX)){
         }                                          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       }                                          exit(1);
    }                                  }else
   }                                          Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
          /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         /* getting the maximum value of the modality of the covariate
   if (popforecast==1) {                                   (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     free_ivector(popage,0,AGESUP);                                   female ies 1, then modmaxcovj=1.*/
     free_vector(popeffectif,0,AGESUP);                          }
     free_vector(popcount,0,AGESUP);                  } /* end for loop on individuals i */
   }      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      cptcode=modmaxcovj;
   fclose(ficrespop);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
 } /* End of popforecast */                  /*for (i=0; i<=cptcode; i++) {*/
       for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
 int fileappend(FILE *fichier, char *optionfich)        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
 {        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
   if((fichier=fopen(optionfich,"a"))==NULL) {        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
     printf("Problem with file: %s\n", optionfich);                                  if( k != -1){
     fprintf(ficlog,"Problem with file: %s\n", optionfich);                                          ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
     return (0);                                                                                                                   covariate for which somebody answered excluding 
   }                                                                                                                   undefined. Usually 2: 0 and 1. */
   fflush(fichier);                                  }
   return (1);                                  ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
 }                                                                                                                                  covariate for which somebody answered including 
                                                                                                                                   undefined. Usually 3: -1, 0 and 1. */
         }
 /**************** function prwizard **********************/        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
 void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)                           * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
 {      } /* Ndum[-1] number of undefined modalities */
                   
   /* Wizard to print covariance matrix template */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
   char ca[32], cb[32], cc[32];         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;         modmincovj=3; modmaxcovj = 7;
   int numlinepar;         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");         defining two dummy variables: variables V1_1 and V1_2.
   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");         nbcode[Tvar[j]][ij]=k;
   for(i=1; i <=nlstate; i++){         nbcode[Tvar[j]][1]=0;
     jj=0;         nbcode[Tvar[j]][2]=1;
     for(j=1; j <=nlstate+ndeath; j++){         nbcode[Tvar[j]][3]=2;
       if(j==i) continue;         To be continued (not working yet).
       jj++;      */
       /*ca[0]= k+'a'-1;ca[1]='\0';*/      ij=0; /* ij is similar to i but can jump over null modalities */
       printf("%1d%1d",i,j);      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*/
       fprintf(ficparo,"%1d%1d",i,j);          if (Ndum[i] == 0) { /* If nobody responded to this modality k */
       for(k=1; k<=ncovmodel;k++){                                  break;
         /*        printf(" %lf",param[i][j][k]); */                          }
         /*        fprintf(ficparo," %lf",param[i][j][k]); */                          ij++;
         printf(" 0.");                          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.*/
         fprintf(ficparo," 0.");                          cptcode = ij; /* New max modality for covar j */
       }      } /* end of loop on modality i=-1 to 1 or more */
       printf("\n");                  
       fprintf(ficparo,"\n");      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
     }      /*  /\*recode from 0 *\/ */
   }      /*                               k is a modality. If we have model=V1+V1*sex  */
   printf("# Scales (for hessian or gradient estimation)\n");      /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");      /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/      /*  } */
   for(i=1; i <=nlstate; i++){      /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
     jj=0;      /*  if (ij > ncodemax[j]) { */
     for(j=1; j <=nlstate+ndeath; j++){      /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       if(j==i) continue;      /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
       jj++;      /*    break; */
       fprintf(ficparo,"%1d%1d",i,j);      /*  } */
       printf("%1d%1d",i,j);      /*   }  /\* end of loop on modality k *\/ */
       fflush(stdout);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       for(k=1; k<=ncovmodel;k++){    
         /*      printf(" %le",delti3[i][j][k]); */          for (k=-1; k< maxncov; k++) Ndum[k]=0; 
         /*      fprintf(ficparo," %le",delti3[i][j][k]); */    
         printf(" 0.");    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
         fprintf(ficparo," 0.");                  /* 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 */ 
       numlinepar++;                  Ndum[ij]++; /* Might be supersed V1 + V1*age */
       printf("\n");          } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
       fprintf(ficparo,"\n");          
     }          ij=0;
   }          for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   printf("# Covariance matrix\n");                  /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
 /* # 121 Var(a12)\n\ */                  if((Ndum[i]!=0) && (i<=ncovcol)){
 /* # 122 Cov(b12,a12) Var(b12)\n\ */                          /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
 /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */                          Tvaraff[++ij]=i; /*For printing (unclear) */
 /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */                  }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
 /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */                          Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
 /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */                  }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
 /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */                          Tvaraff[++ij]=i; /*For printing (unclear) */
 /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */                  }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
   fflush(stdout);                   Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
   fprintf(ficparo,"# Covariance matrix\n");                  }
   /* # 121 Var(a12)\n\ */          } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */          /* ij--; */
   /* #   ...\n\ */          /* cptcoveff=ij; /\*Number of total covariates*\/ */
   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */          *cptcov=ij; /*Number of total real effective covariates: effective
                                                             * because they can be excluded from the model and real
   for(itimes=1;itimes<=2;itimes++){                                                           * if in the model but excluded because missing values*/
     jj=0;  }
     for(i=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){  
         if(j==i) continue;  /*********** Health Expectancies ****************/
         for(k=1; k<=ncovmodel;k++){  
           jj++;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           ca[0]= k+'a'-1;ca[1]='\0';  
           if(itimes==1){  {
             printf("#%1d%1d%d",i,j,k);    /* Health expectancies, no variances */
             fprintf(ficparo,"#%1d%1d%d",i,j,k);    int i, j, nhstepm, hstepm, h, nstepm;
           }else{    int nhstepma, nstepma; /* Decreasing with age */
             printf("%1d%1d%d",i,j,k);    double age, agelim, hf;
             fprintf(ficparo,"%1d%1d%d",i,j,k);    double ***p3mat;
             /*  printf(" %.5le",matcov[i][j]); */    double eip;
           }  
           ll=0;    pstamp(ficreseij);
           for(li=1;li <=nlstate; li++){    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
             for(lj=1;lj <=nlstate+ndeath; lj++){    fprintf(ficreseij,"# Age");
               if(lj==li) continue;    for(i=1; i<=nlstate;i++){
               for(lk=1;lk<=ncovmodel;lk++){      for(j=1; j<=nlstate;j++){
                 ll++;        fprintf(ficreseij," e%1d%1d ",i,j);
                 if(ll<=jj){      }
                   cb[0]= lk +'a'-1;cb[1]='\0';      fprintf(ficreseij," e%1d. ",i);
                   if(ll<jj){    }
                     if(itimes==1){    fprintf(ficreseij,"\n");
                       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{    if(estepm < stepm){
                       printf(" 0.");      printf ("Problem %d lower than %d\n",estepm, stepm);
                       fprintf(ficparo," 0.");    }
                     }    else  hstepm=estepm;   
                   }else{    /* We compute the life expectancy from trapezoids spaced every estepm months
                     if(itimes==1){     * This is mainly to measure the difference between two models: for example
                       printf(" Var(%s%1d%1d)",ca,i,j);     * if stepm=24 months pijx are given only every 2 years and by summing them
                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);     * we are calculating an estimate of the Life Expectancy assuming a linear 
                     }else{     * progression in between and thus overestimating or underestimating according
                       printf(" 0.");     * to the curvature of the survival function. If, for the same date, we 
                       fprintf(ficparo," 0.");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                     }     * to compare the new estimate of Life expectancy with the same linear 
                   }     * hypothesis. A more precise result, taking into account a more precise
                 }     * curvature will be obtained if estepm is as small as stepm. */
               } /* end lk */  
             } /* end lj */    /* For example we decided to compute the life expectancy with the smallest unit */
           } /* end li */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           printf("\n");       nhstepm is the number of hstepm from age to agelim 
           fprintf(ficparo,"\n");       nstepm is the number of stepm from age to agelin. 
           numlinepar++;       Look at hpijx to understand the reason of that which relies in memory size
         } /* end k*/       and note for a fixed period like estepm months */
       } /*end j */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     } /* end i */       survival function given by stepm (the optimization length). Unfortunately it
   } /* end itimes */       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 } /* end of prwizard */       results. So we changed our mind and took the option of the best precision.
 /******************* Gompertz Likelihood ******************************/    */
 double gompertz(double x[])    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 {  
   double A,B,L=0.0,sump=0.,num=0.;    agelim=AGESUP;
   int i,n=0; /* n is the size of the sample */    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   for (i=0;i<=imx-1 ; i++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     sump=sump+weight[i];      
     /*    sump=sump+1;*/  /* nhstepm age range expressed in number of stepm */
     num=num+1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* for (i=0; i<=imx; i++)    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      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 (age=bage; age<=fage; age ++){ 
   for (i=1;i<=imx ; i++)      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       if (cens[i] == 1 && wav[i]>1)      /* if (stepm >= YEARM) hstepm=1;*/
         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
        
       if (cens[i] == 0 && wav[i]>1)      /* If stepm=6 months */
         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))      /* Computed by stepm unit matrices, product of hstepma matrices, stored
              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            
       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       if (wav[i] > 1 ) { /* ??? */      
         L=L+A*weight[i];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         /*      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("%d|",(int)age);fflush(stdout);
     }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   return -2*L*num/sump;        for(j=1; j<=nlstate;j++)
 }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 /******************* Printing html file ***********/            
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \            /* 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]);*/
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,  double p[],double **matcov,double agemortsup){          }
   int i,k;  
       fprintf(ficreseij,"%3.0f",age );
   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");      for(i=1; i<=nlstate;i++){
   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);        eip=0;
   for (i=1;i<=2;i++)        for(j=1; j<=nlstate;j++){
     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]));          eip +=eij[i][j][(int)age];
   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   fprintf(fichtm,"</ul>");        }
         fprintf(ficreseij,"%9.4f", eip );
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");      }
       fprintf(ficreseij,"\n");
  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++)    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);    printf("\n");
     fprintf(ficlog,"\n");
      
   fflush(fichtm);  }
 }  
   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[] )
 /******************* Gnuplot file **************/  
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  {
     /* Covariances of health expectancies eij and of total life expectancies according
   char dirfileres[132],optfileres[132];       to initial status i, ei. .
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    */
   int ng;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   /*#ifdef windows */    double ***p3matp, ***p3matm, ***varhe;
   fprintf(ficgp,"cd \"%s\" \n",pathc);    double **dnewm,**doldm;
     /*#endif */    double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
   strcpy(dirfileres,optionfilefiname);    int theta;
   strcpy(optfileres,"vpl");  
   fprintf(ficgp,"set out \"graphmort.png\"\n ");    double eip, vip;
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");  
   fprintf(ficgp, "set ter png small\n set log y\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   fprintf(ficgp, "set size 0.65,0.65\n");    xp=vector(1,npar);
   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
 }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
 /***********************************************/      for(j=1; j<=nlstate;j++)
 /**************** Main Program *****************/        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 /***********************************************/      fprintf(ficresstdeij," e%1d. ",i);
     }
 int main(int argc, char *argv[])    fprintf(ficresstdeij,"\n");
 {  
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    pstamp(ficrescveij);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   int linei, month, year,iout;    fprintf(ficrescveij,"# Age");
   int jj, ll, li, lj, lk, imk;    for(i=1; i<=nlstate;i++)
   int numlinepar=0; /* Current linenumber of parameter file */      for(j=1; j<=nlstate;j++){
   int itimes;        cptj= (j-1)*nlstate+i;
   int NDIM=2;        for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
   char ca[32], cb[32], cc[32];            cptj2= (j2-1)*nlstate+i2;
   char dummy[]="                         ";            if(cptj2 <= cptj)
   /*  FILE *fichtm; *//* Html File */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   /* FILE *ficgp;*/ /*Gnuplot File */          }
   struct stat info;      }
   double agedeb, agefin,hf;    fprintf(ficrescveij,"\n");
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    
     if(estepm < stepm){
   double fret;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double **xi,tmp,delta;    }
     else  hstepm=estepm;   
   double dum; /* Dummy variable */    /* We compute the life expectancy from trapezoids spaced every estepm months
   double ***p3mat;     * This is mainly to measure the difference between two models: for example
   double ***mobaverage;     * if stepm=24 months pijx are given only every 2 years and by summing them
   int *indx;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   char line[MAXLINE], linepar[MAXLINE];     * progression in between and thus overestimating or underestimating according
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];     * to the curvature of the survival function. If, for the same date, we 
   char pathr[MAXLINE], pathimach[MAXLINE];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   char **bp, *tok, *val; /* pathtot */     * to compare the new estimate of Life expectancy with the same linear 
   int firstobs=1, lastobs=10;     * hypothesis. A more precise result, taking into account a more precise
   int sdeb, sfin; /* Status at beginning and end */     * curvature will be obtained if estepm is as small as stepm. */
   int c,  h , cpt,l;  
   int ju,jl, mi;    /* For example we decided to compute the life expectancy with the smallest unit */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;       nhstepm is the number of hstepm from age to agelim 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */       nstepm is the number of stepm from age to agelin. 
   int mobilav=0,popforecast=0;       Look at hpijx to understand the reason of that which relies in memory size
   int hstepm, nhstepm;       and note for a fixed period like estepm months */
   int agemortsup;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   float  sumlpop=0.;       survival function given by stepm (the optimization length). Unfortunately it
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;       means that if the survival funtion is printed only each two years of age and if
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
   double bage, fage, age, agelim, agebase;    */
   double ftolpl=FTOL;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double **prlim;  
   double *severity;    /* If stepm=6 months */
   double ***param; /* Matrix of parameters */    /* nhstepm age range expressed in number of stepm */
   double  *p;    agelim=AGESUP;
   double **matcov; /* Matrix of covariance */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   double ***delti3; /* Scale */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double *delti; /* Scale */    /* if (stepm >= YEARM) hstepm=1;*/
   double ***eij, ***vareij;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double **varpl; /* Variances of prevalence limits by age */    
   double *epj, vepp;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double kk1, kk2;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   double **ximort;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   int *dcwave;    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   char z[1]="c", occ;    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   char  *strt, strtend[80];      /* if (stepm >= YEARM) hstepm=1;*/
   char *stratrunc;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   int lstra;                  
       /* If stepm=6 months */
   long total_usecs;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 /*   setlocale (LC_ALL, ""); */      
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 /*   textdomain (PACKAGE); */                  
 /*   setlocale (LC_CTYPE, ""); */      /* Computing  Variances of health expectancies */
 /*   setlocale (LC_MESSAGES, ""); */      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for(theta=1; theta <=npar; theta++){
   (void) gettimeofday(&start_time,&tzp);        for(i=1; i<=npar; i++){ 
   curr_time=start_time;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   tm = *localtime(&start_time.tv_sec);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   tmg = *gmtime(&start_time.tv_sec);        }
   strcpy(strstart,asctime(&tm));        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 /*  printf("Localtime (at start)=%s",strstart); */                          
 /*  tp.tv_sec = tp.tv_sec +86400; */        for(j=1; j<= nlstate; j++){
 /*  tm = *localtime(&start_time.tv_sec); */          for(i=1; i<=nlstate; i++){
 /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */            for(h=0; h<=nhstepm-1; h++){
 /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
 /*   tmg.tm_hour=tmg.tm_hour + 1; */              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 /*   tp.tv_sec = mktime(&tmg); */            }
 /*   strt=asctime(&tmg); */          }
 /*   printf("Time(after) =%s",strstart);  */        }
 /*  (void) time (&time_value);                          
 *  printf("time=%d,t-=%d\n",time_value,time_value-86400);        for(ij=1; ij<= nlstate*nlstate; ij++)
 *  tm = *localtime(&time_value);          for(h=0; h<=nhstepm-1; h++){
 *  strstart=asctime(&tm);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);          }
 */      }/* End theta */
       
   nberr=0; /* Number of errors and warnings */      
   nbwarn=0;      for(h=0; h<=nhstepm-1; h++)
   getcwd(pathcd, size);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   printf("\n%s\n%s",version,fullversion);            trgradg[h][j][theta]=gradg[h][theta][j];
   if(argc <=1){      
     printf("\nEnter the parameter file name: ");                  
     fgets(pathr,FILENAMELENGTH,stdin);      for(ij=1;ij<=nlstate*nlstate;ij++)
     i=strlen(pathr);        for(ji=1;ji<=nlstate*nlstate;ji++)
     if(pathr[i-1]=='\n')          varhe[ij][ji][(int)age] =0.;
       pathr[i-1]='\0';                  
    for (tok = pathr; tok != NULL; ){      printf("%d|",(int)age);fflush(stdout);
       printf("Pathr |%s|\n",pathr);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');      for(h=0;h<=nhstepm-1;h++){
       printf("val= |%s| pathr=%s\n",val,pathr);        for(k=0;k<=nhstepm-1;k++){
       strcpy (pathtot, val);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       if(pathr[0] == '\0') break; /* Dirty */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     }          for(ij=1;ij<=nlstate*nlstate;ij++)
   }            for(ji=1;ji<=nlstate*nlstate;ji++)
   else{              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     strcpy(pathtot,argv[1]);        }
   }      }
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/                  
   /*cygwin_split_path(pathtot,path,optionfile);      /* Computing expectancies */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   /* cutv(path,optionfile,pathtot,'\\');*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   /* Split argv[0], imach program to get pathimach */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   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);            /* 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]);*/
  /*   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);      fprintf(ficresstdeij,"%3.0f",age );
   chdir(path); /* Can be a relative path */      for(i=1; i<=nlstate;i++){
   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */        eip=0.;
     printf("Current directory %s!\n",pathcd);        vip=0.;
   strcpy(command,"mkdir ");        for(j=1; j<=nlstate;j++){
   strcat(command,optionfilefiname);          eip += eij[i][j][(int)age];
   if((outcmd=system(command)) != 0){          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     /* fclose(ficlog); */        }
 /*     exit(1); */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   }      }
 /*   if((imk=mkdir(optionfilefiname))<0){ */      fprintf(ficresstdeij,"\n");
 /*     perror("mkdir"); */                  
 /*   } */      fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
   /*-------- arguments in the command line --------*/        for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
   /* Log file */          for(i2=1; i2<=nlstate;i2++)
   strcat(filelog, optionfilefiname);            for(j2=1; j2<=nlstate;j2++){
   strcat(filelog,".log");    /* */              cptj2= (j2-1)*nlstate+i2;
   if((ficlog=fopen(filelog,"w"))==NULL)    {              if(cptj2 <= cptj)
     printf("Problem with logfile %s\n",filelog);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     goto end;            }
   }        }
   fprintf(ficlog,"Log filename:%s\n",filelog);      fprintf(ficrescveij,"\n");
   fprintf(ficlog,"\n%s\n%s",version,fullversion);                  
   fprintf(ficlog,"\nEnter the parameter file name: \n");    }
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
  path=%s \n\    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  optionfile=%s\n\    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
  optionfilext=%s\n\    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Local time (at start):%s",strstart);    printf("\n");
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"\n");
   fflush(ficlog);          
 /*   (void) gettimeofday(&curr_time,&tzp); */    free_vector(xm,1,npar);
 /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /* */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   strcpy(fileres,"r");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   strcat(fileres, optionfilefiname);  }
   strcat(fileres,".txt");    /* Other files have txt extension */   
   /************ Variance ******************/
   /*---------arguments file --------*/   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[])
    {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     /* Variance of health expectancies */
     printf("Problem with optionfile %s\n",optionfile);     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);     /* double **newm;*/
     fflush(ficlog);     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     goto end;    
   }     /* int movingaverage(); */
      double **dnewm,**doldm;
      double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   strcpy(filereso,"o");     int k;
   strcat(filereso,fileres);     double *xp;
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */     double **gp, **gm;  /* for var eij */
     printf("Problem with Output resultfile: %s\n", filereso);     double ***gradg, ***trgradg; /*for var eij */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);     double **gradgp, **trgradgp; /* for var p point j */
     fflush(ficlog);     double *gpp, *gmp; /* for var p point j */
     goto end;     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   }     double ***p3mat;
      double age,agelim, hf;
   /* Reads comments: lines beginning with '#' */     /* double ***mobaverage; */
   numlinepar=0;     int theta;
   while((c=getc(ficpar))=='#' && c!= EOF){     char digit[4];
     ungetc(c,ficpar);     char digitp[25];
     fgets(line, MAXLINE, ficpar);  
     numlinepar++;     char fileresprobmorprev[FILENAMELENGTH];
     puts(line);  
     fputs(line,ficparo);     if(popbased==1){
     fputs(line,ficlog);       if(mobilav!=0)
   }         strcpy(digitp,"-POPULBASED-MOBILAV_");
   ungetc(c,ficpar);       else strcpy(digitp,"-POPULBASED-NOMOBIL_");
      }
   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);     else 
   numlinepar++;       strcpy(digitp,"-STABLBASED_");
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);  
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);     /* if (mobilav!=0) { */
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);     /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fflush(ficlog);     /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
   while((c=getc(ficpar))=='#' && c!= EOF){     /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
     ungetc(c,ficpar);     /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
     fgets(line, MAXLINE, ficpar);     /*   } */
     numlinepar++;     /* } */
     puts(line);  
     fputs(line,ficparo);     strcpy(fileresprobmorprev,"PRMORPREV-"); 
     fputs(line,ficlog);     sprintf(digit,"%-d",ij);
   }     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   ungetc(c,ficpar);     strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         strcat(fileresprobmorprev,fileresu);
   covar=matrix(0,NCOVMAX,1,n);     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/     pstamp(ficresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   delti=delti3[1][1];     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/       fprintf(ficresprobmorprev," p.%-d SE",j);
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */       for(i=1; i<=nlstate;i++)
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     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);     fprintf(ficresprobmorprev,"\n");
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     fclose (ficparo);     fprintf(ficgp,"\n# Routine varevsij");
     fclose (ficlog);     fprintf(ficgp,"\nunset title \n");
     goto end;     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     exit(0);     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   }     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   else if(mle==-3) {     /*   } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);     pstamp(ficresvij);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     if(popbased==1)
     matcov=matrix(1,npar,1,npar);       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   }     else
   else{       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     /* Read guess parameters */     fprintf(ficresvij,"# Age");
     /* Reads comments: lines beginning with '#' */     for(i=1; i<=nlstate;i++)
     while((c=getc(ficpar))=='#' && c!= EOF){       for(j=1; j<=nlstate;j++)
       ungetc(c,ficpar);         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       fgets(line, MAXLINE, ficpar);     fprintf(ficresvij,"\n");
       numlinepar++;  
       puts(line);     xp=vector(1,npar);
       fputs(line,ficparo);     dnewm=matrix(1,nlstate,1,npar);
       fputs(line,ficlog);     doldm=matrix(1,nlstate,1,nlstate);
     }     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     ungetc(c,ficpar);     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     for(i=1; i <=nlstate; i++){     gpp=vector(nlstate+1,nlstate+ndeath);
       j=0;     gmp=vector(nlstate+1,nlstate+ndeath);
       for(jj=1; jj <=nlstate+ndeath; jj++){     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         if(jj==i) continue;    
         j++;     if(estepm < stepm){
         fscanf(ficpar,"%1d%1d",&i1,&j1);       printf ("Problem %d lower than %d\n",estepm, stepm);
         if ((i1 != i) && (j1 != j)){     }
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \     else  hstepm=estepm;   
 It might be a problem of design; if ncovcol and the model are correct\n \     /* For example we decided to compute the life expectancy with the smallest unit */
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           exit(1);        nhstepm is the number of hstepm from age to agelim 
         }        nstepm is the number of stepm from age to agelim. 
         fprintf(ficparo,"%1d%1d",i1,j1);        Look at function hpijx to understand why because of memory size limitations, 
         if(mle==1)        we decided (b) to get a life expectancy respecting the most precise curvature of the
           printf("%1d%1d",i,j);        survival function given by stepm (the optimization length). Unfortunately it
         fprintf(ficlog,"%1d%1d",i,j);        means that if the survival funtion is printed every two years of age and if
         for(k=1; k<=ncovmodel;k++){        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fscanf(ficpar," %lf",&param[i][j][k]);        results. So we changed our mind and took the option of the best precision.
           if(mle==1){     */
             printf(" %lf",param[i][j][k]);     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             fprintf(ficlog," %lf",param[i][j][k]);     agelim = AGESUP;
           }     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           else       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             fprintf(ficlog," %lf",param[i][j][k]);       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficparo," %lf",param[i][j][k]);       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         fscanf(ficpar,"\n");       gp=matrix(0,nhstepm,1,nlstate);
         numlinepar++;       gm=matrix(0,nhstepm,1,nlstate);
         if(mle==1)                  
           printf("\n");                  
         fprintf(ficlog,"\n");       for(theta=1; theta <=npar; theta++){
         fprintf(ficparo,"\n");         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }           }
     fflush(ficlog);                          
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
     p=param[1][1];                          
             if (popbased==1) {
     /* Reads comments: lines beginning with '#' */           if(mobilav ==0){
     while((c=getc(ficpar))=='#' && c!= EOF){             for(i=1; i<=nlstate;i++)
       ungetc(c,ficpar);               prlim[i][i]=probs[(int)age][i][ij];
       fgets(line, MAXLINE, ficpar);           }else{ /* mobilav */ 
       numlinepar++;             for(i=1; i<=nlstate;i++)
       puts(line);               prlim[i][i]=mobaverage[(int)age][i][ij];
       fputs(line,ficparo);           }
       fputs(line,ficlog);         }
     }                          
     ungetc(c,ficpar);         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
          for(j=1; j<= nlstate; j++){
     for(i=1; i <=nlstate; i++){           for(h=0; h<=nhstepm; h++){
       for(j=1; j <=nlstate+ndeath-1; j++){             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         fscanf(ficpar,"%1d%1d",&i1,&j1);               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         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);         /* Next for computing probability of death (h=1 means
         }            computed over hstepm matrices product = hstepm*stepm months) 
         printf("%1d%1d",i,j);            as a weighted average of prlim.
         fprintf(ficparo,"%1d%1d",i1,j1);         */
         fprintf(ficlog,"%1d%1d",i1,j1);         for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(k=1; k<=ncovmodel;k++){           for(i=1,gpp[j]=0.; i<= nlstate; i++)
           fscanf(ficpar,"%le",&delti3[i][j][k]);             gpp[j] += prlim[i][i]*p3mat[i][j][1];
           printf(" %le",delti3[i][j][k]);         }    
           fprintf(ficparo," %le",delti3[i][j][k]);         /* end probability of death */
           fprintf(ficlog," %le",delti3[i][j][k]);                          
         }         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         fscanf(ficpar,"\n");           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         numlinepar++;                          
         printf("\n");         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
         fprintf(ficparo,"\n");                          
         fprintf(ficlog,"\n");         if (popbased==1) {
       }           if(mobilav ==0){
     }             for(i=1; i<=nlstate;i++)
     fflush(ficlog);               prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
     delti=delti3[1][1];             for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
     /* 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 '#' */         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     while((c=getc(ficpar))=='#' && c!= EOF){                          
       ungetc(c,ficpar);         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
       fgets(line, MAXLINE, ficpar);           for(h=0; h<=nhstepm; h++){
       numlinepar++;             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       puts(line);               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fputs(line,ficparo);           }
       fputs(line,ficlog);         }
     }         /* This for computing probability of death (h=1 means
     ungetc(c,ficpar);            computed over hstepm matrices product = hstepm*stepm months) 
              as a weighted average of prlim.
     matcov=matrix(1,npar,1,npar);         */
     for(i=1; i <=npar; i++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fscanf(ficpar,"%s",&str);           for(i=1,gmp[j]=0.; i<= nlstate; i++)
       if(mle==1)             gmp[j] += prlim[i][i]*p3mat[i][j][1];
         printf("%s",str);         }    
       fprintf(ficlog,"%s",str);         /* end probability of death */
       fprintf(ficparo,"%s",str);                          
       for(j=1; j <=i; j++){         for(j=1; j<= nlstate; j++) /* vareij */
         fscanf(ficpar," %le",&matcov[i][j]);           for(h=0; h<=nhstepm; h++){
         if(mle==1){             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           printf(" %.5le",matcov[i][j]);           }
         }                          
         fprintf(ficlog," %.5le",matcov[i][j]);         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         fprintf(ficparo," %.5le",matcov[i][j]);           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }         }
       fscanf(ficpar,"\n");                          
       numlinepar++;       } /* End theta */
       if(mle==1)                  
         printf("\n");       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fprintf(ficlog,"\n");                  
       fprintf(ficparo,"\n");       for(h=0; h<=nhstepm; h++) /* veij */
     }         for(j=1; j<=nlstate;j++)
     for(i=1; i <=npar; i++)           for(theta=1; theta <=npar; theta++)
       for(j=i+1;j<=npar;j++)             trgradg[h][j][theta]=gradg[h][theta][j];
         matcov[i][j]=matcov[j][i];                  
           for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     if(mle==1)         for(theta=1; theta <=npar; theta++)
       printf("\n");           trgradgp[j][theta]=gradgp[theta][j];
     fprintf(ficlog,"\n");                  
                      
     fflush(ficlog);       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for(i=1;i<=nlstate;i++)
     /*-------- Rewriting parameter file ----------*/         for(j=1;j<=nlstate;j++)
     strcpy(rfileres,"r");    /* "Rparameterfile */           vareij[i][j][(int)age] =0.;
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                  
     strcat(rfileres,".");    /* */       for(h=0;h<=nhstepm;h++){
     strcat(rfileres,optionfilext);    /* Other files have txt extension */         for(k=0;k<=nhstepm;k++){
     if((ficres =fopen(rfileres,"w"))==NULL) {           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;           for(i=1;i<=nlstate;i++)
     }             for(j=1;j<=nlstate;j++)
     fprintf(ficres,"#%s\n",version);               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   }    /* End of mle != -3 */         }
        }
   /*-------- data file ----------*/                  
   if((fic=fopen(datafile,"r"))==NULL)    {       /* pptj */
     printf("Problem while opening datafile: %s\n", datafile);goto end;       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   }       for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
   n= lastobs;           varppt[j][i]=doldmp[j][i];
   severity = vector(1,maxwav);       /* end ppptj */
   outcome=imatrix(1,maxwav+1,1,n);       /*  x centered again */
   num=lvector(1,n);                  
   moisnais=vector(1,n);       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
   annais=vector(1,n);                  
   moisdc=vector(1,n);       if (popbased==1) {
   andc=vector(1,n);         if(mobilav ==0){
   agedc=vector(1,n);           for(i=1; i<=nlstate;i++)
   cod=ivector(1,n);             prlim[i][i]=probs[(int)age][i][ij];
   weight=vector(1,n);         }else{ /* mobilav */ 
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */           for(i=1; i<=nlstate;i++)
   mint=matrix(1,maxwav,1,n);             prlim[i][i]=mobaverage[(int)age][i][ij];
   anint=matrix(1,maxwav,1,n);         }
   s=imatrix(1,maxwav+1,1,n);       }
   tab=ivector(1,NCOVMAX);                  
   ncodemax=ivector(1,8);       /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   i=1;          as a weighted average of prlim.
   linei=0;       */
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     linei=linei+1;       for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       if(line[j] == '\t')           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         line[j] = ' ';       }    
     }       /* end probability of death */
     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){                  
       ;       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     };       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     line[j+1]=0;  /* Trims blanks at end of line */         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     if(line[0]=='#'){         for(i=1; i<=nlstate;i++){
       fprintf(ficlog,"Comment line\n%s\n",line);           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       printf("Comment line\n%s\n",line);         }
       continue;       } 
     }       fprintf(ficresprobmorprev,"\n");
                   
     for (j=maxwav;j>=1;j--){       fprintf(ficresvij,"%.0f ",age );
       cutv(stra, strb,line,' ');       for(i=1; i<=nlstate;i++)
       errno=0;         for(j=1; j<=nlstate;j++){
       lval=strtol(strb,&endptr,10);           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/         }
       if( strb[0]=='\0' || (*endptr != '\0')){       fprintf(ficresvij,"\n");
         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);       free_matrix(gp,0,nhstepm,1,nlstate);
         exit(1);       free_matrix(gm,0,nhstepm,1,nlstate);
       }       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       s[j][i]=lval;       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       strcpy(line,stra);     } /* End age */
       cutv(stra, strb,line,' ');     free_vector(gpp,nlstate+1,nlstate+ndeath);
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){     free_vector(gmp,nlstate+1,nlstate+ndeath);
       }     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       else  if(iout=sscanf(strb,"%s.") != 0){     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         month=99;     /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
         year=9999;     fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
       }else{     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         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(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         exit(1);     fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
       }     /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       anint[j][i]= (double) year;     /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       mint[j][i]= (double)month;     /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       strcpy(line,stra);     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     } /* ENd Waves */     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
         fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     cutv(stra, strb,line,' ');     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
     }     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
     else  if(iout=sscanf(strb,"%s.",dummy) != 0){      */
       month=99;     /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
       year=9999;     fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
     }else{  
       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);     free_vector(xp,1,npar);
       exit(1);     free_matrix(doldm,1,nlstate,1,nlstate);
     }     free_matrix(dnewm,1,nlstate,1,npar);
     andc[i]=(double) year;     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     moisdc[i]=(double) month;     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     strcpy(line,stra);     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     cutv(stra, strb,line,' ');     fclose(ficresprobmorprev);
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){     fflush(ficgp);
     }     fflush(fichtm); 
     else  if(iout=sscanf(strb,"%s.") != 0){   }  /* end varevsij */
       month=99;  
       year=9999;  /************ Variance of prevlim ******************/
     }else{   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[])
       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);    /* 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);*/
     annais[i]=(double)(year);  
     moisnais[i]=(double)(month);    double **dnewm,**doldm;
     strcpy(line,stra);    int i, j, nhstepm, hstepm;
        double *xp;
     cutv(stra, strb,line,' ');    double *gp, *gm;
     errno=0;    double **gradg, **trgradg;
     dval=strtod(strb,&endptr);    double **mgm, **mgp;
     if( strb[0]=='\0' || (*endptr != '\0')){    double age,agelim;
       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);    int theta;
       exit(1);    
     }    pstamp(ficresvpl);
     weight[i]=dval;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     strcpy(line,stra);    fprintf(ficresvpl,"# Age");
        for(i=1; i<=nlstate;i++)
     for (j=ncovcol;j>=1;j--){        fprintf(ficresvpl," %1d-%1d",i,i);
       cutv(stra, strb,line,' ');    fprintf(ficresvpl,"\n");
       errno=0;  
       lval=strtol(strb,&endptr,10);    xp=vector(1,npar);
       if( strb[0]=='\0' || (*endptr != '\0')){    dnewm=matrix(1,nlstate,1,npar);
         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);    doldm=matrix(1,nlstate,1,nlstate);
         exit(1);    
       }    hstepm=1*YEARM; /* Every year of age */
       if(lval <-1 || lval >1){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \    agelim = AGESUP;
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  For example, for multinomial values like 1, 2 and 3,\n \      if (stepm >= YEARM) hstepm=1;
  build V1=0 V2=0 for the reference value (1),\n \      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         V1=1 V2=0 for (2) \n \      gradg=matrix(1,npar,1,nlstate);
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \      mgp=matrix(1,npar,1,nlstate);
  output of IMaCh is often meaningless.\n \      mgm=matrix(1,npar,1,nlstate);
  Exiting.\n",lval,linei, i,line,j);      gp=vector(1,nlstate);
         exit(1);      gm=vector(1,nlstate);
       }  
       covar[j][i]=(double)(lval);      for(theta=1; theta <=npar; theta++){
       strcpy(line,stra);        for(i=1; i<=npar; i++){ /* Computes gradient */
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     lstra=strlen(stra);        }
            if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
       stratrunc = &(stra[lstra-9]);        else
       num[i]=atol(stratrunc);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
     }        for(i=1;i<=nlstate;i++){
     else          gp[i] = prlim[i][i];
       num[i]=atol(stra);          mgp[theta][i] = prlim[i][i];
     /*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;}*/        for(i=1; i<=npar; i++) /* Computes gradient */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     i=i+1;        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
   } /* End loop reading  data */          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
   fclose(fic);        else
   /* printf("ii=%d", ij);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
      scanf("%d",i);*/        for(i=1;i<=nlstate;i++){
   imx=i-1; /* Number of individuals */          gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
   /* for (i=1; i<=imx; i++){        }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        for(i=1;i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
     }*/      } /* End theta */
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;      trgradg =matrix(1,nlstate,1,npar);
      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
        for(j=1; j<=nlstate;j++)
   /* for (i=1; i<=imx; i++) */        for(theta=1; theta <=npar; theta++)
            trgradg[j][theta]=gradg[theta][j];
    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;      /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
      else weight[i]=1;*/      /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
   /* Calculation of the number of parameters from char model */      /*  printf(" %d ",j); */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */      /*  for(theta=1; theta <=npar; theta++) */
   Tprod=ivector(1,15);      /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
   Tvaraff=ivector(1,15);      /*  printf("\n "); */
   Tvard=imatrix(1,15,1,2);      /*   } */
   Tage=ivector(1,15);            /* } */
          /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
   if (strlen(model) >1){ /* If there is at least 1 covariate */      /*   printf("\n gradg %d ",(int)age); */
     j=0, j1=0, k1=1, k2=1;      /*   for(j=1; j<=nlstate;j++){ */
     j=nbocc(model,'+'); /* j=Number of '+' */      /*  printf("%d ",j); */
     j1=nbocc(model,'*'); /* j1=Number of '*' */      /*  for(theta=1; theta <=npar; theta++) */
     cptcovn=j+1;      /*    printf("%d %lf ",theta,gradg[theta][j]); */
     cptcovprod=j1; /*Number of products */      /*  printf("\n "); */
          /*   } */
     strcpy(modelsav,model);      /* } */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);      for(i=1;i<=nlstate;i++)
       fprintf(ficlog,"Error. Non available option model=%s ",model);        varpl[i][(int)age] =0.;
       goto end;      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     /* This loop fills the array Tvar from the string 'model'.*/      }else{
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     for(i=(j+1); i>=1;i--){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */      }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */      for(i=1;i<=nlstate;i++)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  /* Model includes a product */      fprintf(ficresvpl,"%.0f ",age );
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/      for(i=1; i<=nlstate;i++)
         if (strcmp(strc,"age")==0) { /* Vn*age */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           cptcovprod--;      fprintf(ficresvpl,"\n");
           cutv(strb,stre,strd,'V');      free_vector(gp,1,nlstate);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/      free_vector(gm,1,nlstate);
           cptcovage++;      free_matrix(mgm,1,npar,1,nlstate);
             Tage[cptcovage]=i;      free_matrix(mgp,1,npar,1,nlstate);
             /*printf("stre=%s ", stre);*/      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    } /* End age */
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    free_vector(xp,1,npar);
           Tvar[i]=atoi(stre);    free_matrix(doldm,1,nlstate,1,npar);
           cptcovage++;    free_matrix(dnewm,1,nlstate,1,nlstate);
           Tage[cptcovage]=i;  
         }  }
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  /************ Variance of one-step probabilities  ******************/
           Tvar[i]=ncovcol+k1;  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[])
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */   {
           Tprod[k1]=i;     int i, j=0,  k1, l1, tj;
           Tvard[k1][1]=atoi(strc); /* m*/     int k2, l2, j1,  z1;
           Tvard[k1][2]=atoi(stre); /* n */     int k=0, l;
           Tvar[cptcovn+k2]=Tvard[k1][1];     int first=1, first1, first2;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           for (k=1; k<=lastobs;k++)     double **dnewm,**doldm;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     double *xp;
           k1++;     double *gp, *gm;
           k2=k2+2;     double **gradg, **trgradg;
         }     double **mu;
       }     double age, cov[NCOVMAX+1];
       else { /* no more sum */     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     int theta;
        /*  scanf("%d",i);*/     char fileresprob[FILENAMELENGTH];
       cutv(strd,strc,strb,'V');     char fileresprobcov[FILENAMELENGTH];
       Tvar[i]=atoi(strc);     char fileresprobcor[FILENAMELENGTH];
       }     double ***varpij;
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);     strcpy(fileresprob,"PROB_"); 
         scanf("%d",i);*/     strcat(fileresprob,fileres);
     } /* end of loop + */     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   } /* end model */       printf("Problem with resultfile: %s\n", fileresprob);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   /*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*/     strcpy(fileresprobcov,"PROBCOV_"); 
      strcat(fileresprobcov,fileresu);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   printf("cptcovprod=%d ", cptcovprod);       printf("Problem with resultfile: %s\n", fileresprobcov);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   scanf("%d ",i);*/     strcpy(fileresprobcor,"PROBCOR_"); 
      strcat(fileresprobcor,fileresu);
     /*  if(mle==1){*/     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if (weightopt != 1) { /* Maximisation without weights*/       printf("Problem with resultfile: %s\n", fileresprobcor);
     for(i=1;i<=n;i++) weight[i]=1.0;       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }     }
     /*-calculation of age at interview from date of interview and age at death -*/     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   agev=matrix(1,maxwav,1,imx);     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);
   for (i=1; i<=imx; i++) {     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(m=2; (m<= maxwav); m++) {     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         anint[m][i]=9999;     pstamp(ficresprob);
         s[m][i]=-1;     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       }     fprintf(ficresprob,"# Age");
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){     pstamp(ficresprobcov);
         nberr++;     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);     fprintf(ficresprobcov,"# Age");
         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);     pstamp(ficresprobcor);
         s[m][i]=-1;     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       }     fprintf(ficresprobcor,"# Age");
       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]);     for(i=1; i<=nlstate;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]);       for(j=1; j<=(nlstate+ndeath);j++){
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       }         fprintf(ficresprobcov," p%1d-%1d ",i,j);
     }         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   }       }  
      /* fprintf(ficresprob,"\n");
   for (i=1; i<=imx; i++)  {        fprintf(ficresprobcov,"\n");
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        fprintf(ficresprobcor,"\n");
     for(m=firstpass; (m<= lastpass); m++){     */
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){     xp=vector(1,npar);
         if (s[m][i] >= nlstate+1) {     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           if(agedc[i]>0)     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               agev[m][i]=agedc[i];     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/     first=1;
             else {     fprintf(ficgp,"\n# Routine varprob");
               if ((int)andc[i]!=9999){     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                 nbwarn++;     fprintf(fichtm,"\n");
                 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);     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);
                 agev[m][i]=-1;     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
               }     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
             }  and drawn. It helps understanding how is the covariance between two incidences.\
         }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         else if(s[m][i] !=9){ /* Standard case, age in fractional     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. \
                                  years but with the precision of a month */  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)  standard deviations wide on each axis. <br>\
             agev[m][i]=1;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           else if(agev[m][i] <agemin){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             agemin=agev[m][i];  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
           }     cov[1]=1;
           else if(agev[m][i] >agemax){     /* tj=cptcoveff; */
             agemax=agev[m][i];     tj = (int) pow(2,nqveff);
             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           }     j1=0;
           /*agev[m][i]=anint[m][i]-annais[i];*/     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
           /*     agev[m][i] = age[i]+2*m;*/       if  (cptcovn>0) {
         }         fprintf(ficresprob, "\n#********** Variable "); 
         else { /* =9 */         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           agev[m][i]=1;         fprintf(ficresprob, "**********\n#\n");
           s[m][i]=-1;         fprintf(ficresprobcov, "\n#********** Variable "); 
         }         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       }         fprintf(ficresprobcov, "**********\n#\n");
       else /*= 0 Unknown */                          
         agev[m][i]=1;         fprintf(ficgp, "\n#********** Variable "); 
     }         for (z1=1; z1<=nqveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficgp, "**********\n#\n");
   }                          
   for (i=1; i<=imx; i++)  {                          
     for(m=firstpass; (m<=lastpass); m++){         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       if (s[m][i] > (nlstate+ndeath)) {         for (z1=1; z1<=nqveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         nberr++;         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         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);             fprintf(ficresprobcor, "\n#********** Variable ");    
         goto end;         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       }         fprintf(ficresprobcor, "**********\n#");    
     }         if(invalidvarcomb[j1]){
   }           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
            fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
   /*for (i=1; i<=imx; i++){           continue;
   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]);       }
 }       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 }*/       gp=vector(1,(nlstate)*(nlstate+ndeath));
        gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){ 
   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);         cov[2]=age;
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);         if(nagesqr==1)
            cov[3]= age*age;
   agegomp=(int)agemin;         for (k=1; k<=cptcovn;k++) {
   free_vector(severity,1,maxwav);           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
   free_imatrix(outcome,1,maxwav+1,1,n);           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
   free_vector(moisnais,1,n);                                                                      * 1  1 1 1 1
   free_vector(annais,1,n);                                                                      * 2  2 1 1 1
   /* free_matrix(mint,1,maxwav,1,n);                                                                      * 3  1 2 1 1
      free_matrix(anint,1,maxwav,1,n);*/                                                                      */
   free_vector(moisdc,1,n);           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
   free_vector(andc,1,n);         }
          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
             for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
   wav=ivector(1,imx);         for (k=1; k<=cptcovprod;k++)
   dh=imatrix(1,lastpass-firstpass+1,1,imx);           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
   bh=imatrix(1,lastpass-firstpass+1,1,imx);                          
   mw=imatrix(1,lastpass-firstpass+1,1,imx);                          
             for(theta=1; theta <=npar; theta++){
   /* Concatenates waves */           for(i=1; i<=npar; i++)
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */           pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                   
   Tcode=ivector(1,100);           k=0;
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);           for(i=1; i<= (nlstate); i++){
   ncodemax[1]=1;             for(j=1; j<=(nlstate+ndeath);j++){
   if (cptcovn > 0) tricode(Tvar,nbcode,imx);               k=k+1;
                     gp[k]=pmmij[i][j];
   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of             }
                                  the estimations*/           }
   h=0;                                  
   m=pow(2,cptcoveff);           for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   for(k=1;k<=cptcoveff; k++){                                  
     for(i=1; i <=(m/pow(2,k));i++){           pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for(j=1; j <= ncodemax[k]; j++){           k=0;
         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){           for(i=1; i<=(nlstate); i++){
           h++;             for(j=1; j<=(nlstate+ndeath);j++){
           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;               k=k+1;
           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/               gm[k]=pmmij[i][j];
         }             }
       }           }
     }                                  
   }           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
      codtab[1][2]=1;codtab[2][2]=2; */         }
   /* for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);           for(theta=1; theta <=npar; theta++)
      }             trgradg[j][theta]=gradg[theta][j];
      printf("\n");                          
      }         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
      scanf("%d",i);*/         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                              
   /*------------ gnuplot -------------*/         pmij(pmmij,cov,ncovmodel,x,nlstate);
   strcpy(optionfilegnuplot,optionfilefiname);                          
   if(mle==-3)         k=0;
     strcat(optionfilegnuplot,"-mort");         for(i=1; i<=(nlstate); i++){
   strcat(optionfilegnuplot,".gp");           for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {             mu[k][(int) age]=pmmij[i][j];
     printf("Problem with file %s",optionfilegnuplot);           }
   }         }
   else{         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     fprintf(ficgp,"\n# %s\n", version);           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     fprintf(ficgp,"# %s\n", optionfilegnuplot);             varpij[i][j][(int)age] = doldm[i][j];
     fprintf(ficgp,"set missing 'NaNq'\n");                          
   }         /*printf("\n%d ",(int)age);
   /*  fclose(ficgp);*/           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /*--------- index.htm --------*/           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */           }*/
   if(mle==-3)                          
     strcat(optionfilehtm,"-mort");         fprintf(ficresprob,"\n%d ",(int)age);
   strcat(optionfilehtm,".htm");         fprintf(ficresprobcov,"\n%d ",(int)age);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {         fprintf(ficresprobcor,"\n%d ",(int)age);
     printf("Problem with %s \n",optionfilehtm), exit(0);                          
   }         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   strcat(optionfilehtmcov,"-cov.htm");           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     printf("Problem with %s \n",optionfilehtmcov), exit(0);         }
   }         i=0;
   else{         for (k=1; k<=(nlstate);k++){
   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \           for (l=1; l<=(nlstate+ndeath);l++){ 
 <hr size=\"2\" color=\"#EC5E5E\"> \n\             i++;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   }             for (j=1; j<=i;j++){
                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 <hr size=\"2\" color=\"#EC5E5E\"> \n\               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\             }
 \n\           }
 <hr  size=\"2\" color=\"#EC5E5E\">\         }/* end of loop for state */
  <ul><li><h4>Parameter files</h4>\n\       } /* end of loop for age */
  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  - Date and time at start: %s</ul>\n",\      
           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\       /* Confidence intervalle of pij  */
           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\       /*
           fileres,fileres,\         fprintf(ficgp,"\nunset parametric;unset label");
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   fflush(fichtm);         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);
   strcpy(pathr,path);         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   strcat(pathr,optionfilefiname);         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   chdir(optionfilefiname); /* Move to directory named optionfile */         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   /* Calculates basic frequencies. Computes observed prevalence at single age                  
      and prints on file fileres'p'. */       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);       first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
   fprintf(fichtm,"\n");         for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\           if(l2==k2) continue;
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\           j=(k2-1)*(nlstate+ndeath)+l2;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\           for (k1=1; k1<=(nlstate);k1++){
           imx,agemin,agemax,jmin,jmax,jmean);             for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               if(l1==k1) continue;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               i=(k1-1)*(nlstate+ndeath)+l1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               if(i<=j) continue;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               for (age=bage; age<=fage; age ++){ 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                 if ((int)age %5==0){
                       v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                       v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /* For Powell, parameters are in a vector p[] starting at p[1]                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                   mu1=mu[i][(int) age]/stepm*YEARM ;
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */                   mu2=mu[j][(int) age]/stepm*YEARM;
                    c12=cv12/sqrt(v1*v2);
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/                   /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   if (mle==-3){                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ximort=matrix(1,NDIM,1,NDIM);                   if ((lc2 <0) || (lc1 <0) ){
     cens=ivector(1,n);                     if(first2==1){
     ageexmed=vector(1,n);                       first1=0;
     agecens=vector(1,n);                       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);
     dcwave=ivector(1,n);                     }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
     for (i=1; i<=imx; i++){                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
       dcwave[i]=-1;                     /* lc2=fabs(lc2); */
       for (m=firstpass; m<=lastpass; m++)                   }
         if (s[m][i]>nlstate) {                                                                  
           dcwave[i]=m;                   /* Eigen vectors */
           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           break;                   /*v21=sqrt(1.-v11*v11); *//* error */
         }                   v21=(lc1-v1)/cv12*v11;
     }                   v12=-v21;
                    v22=v11;
     for (i=1; i<=imx; i++) {                   tnalp=v21/v11;
       if (wav[i]>0){                   if(first1==1){
         ageexmed[i]=agev[mw[1][i]][i];                     first1=0;
         j=wav[i];                     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);
         agecens[i]=1.;                   }
                    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);
         if (ageexmed[i]> 1 && wav[i] > 0){                   /*printf(fignu*/
           agecens[i]=agev[mw[j][i]][i];                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           cens[i]= 1;                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         }else if (ageexmed[i]< 1)                   if(first==1){
           cens[i]= -1;                     first=0;
         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
           cens[i]=0 ;                     fprintf(ficgp,"\nset parametric;unset label");
       }                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
       else cens[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\">                                                                                                                                           \
     for (i=1;i<=NDIM;i++) {  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
       for (j=1;j<=NDIM;j++)                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
         ximort[i][j]=(i == j ? 1.0 : 0.0);                             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);
     p[1]=0.0268; p[NDIM]=0.083;                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
     /*printf("%lf %lf", p[1], p[2]);*/                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                         fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                         fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
     printf("Powell\n");  fprintf(ficlog,"Powell\n");                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
     strcpy(filerespow,"pow-mort");                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     strcat(filerespow,fileres);                   }else{
     if((ficrespow=fopen(filerespow,"w"))==NULL) {                     first=0;
       printf("Problem with resultfile: %s\n", filerespow);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     }                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fprintf(ficrespow,"# Powell\n# iter -2*LL");                     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 (i=1;i<=nlstate;i++)                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
         for(j=1;j<=nlstate+ndeath;j++)                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);                   }/* if first */
     */                 } /* age mod 5 */
     fprintf(ficrespow,"\n");               } /* 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);
     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);               first=1;
     fclose(ficrespow);             } /*l12 */
               } /* k12 */
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);         } /*l1 */
        }/* k1 */
     for(i=1; i <=NDIM; i++)     }  /* loop on combination of covariates j1 */
       for(j=i+1;j<=NDIM;j++)     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         matcov[i][j]=matcov[j][i];     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     printf("\nCovariance matrix\n ");     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     for(i=1; i <=NDIM; i++) {     free_vector(xp,1,npar);
       for(j=1;j<=NDIM;j++){     fclose(ficresprob);
         printf("%f ",matcov[i][j]);     fclose(ficresprobcov);
       }     fclose(ficresprobcor);
       printf("\n ");     fflush(ficgp);
     }     fflush(fichtmcov);
       }
     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]));  /******************* Printing html file ***********/
   void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
     lsurv=vector(1,AGESUP);                    int lastpass, int stepm, int weightopt, char model[],\
     lpop=vector(1,AGESUP);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     tpop=vector(1,AGESUP);                    int popforecast, int prevfcast, int backcast, int estepm , \
     lsurv[agegomp]=100000;                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                        double jprev2, double mprev2,double anprev2, double dateprev2){
     for (k=agegomp;k<=AGESUP;k++) {    int jj1, k1, i1, cpt;
       agemortsup=k;  
       if (p[1]*exp(p[2]*(k-agegomp))>1) break;     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     }     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
      </ul>");
     for (k=agegomp;k<agemortsup;k++)     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
                 jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
     for (k=agegomp;k<agemortsup;k++){     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) ",
       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
       sumlpop=sumlpop+lpop[k];     fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     }     fprintf(fichtm,"\
       - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     tpop[agegomp]=sumlpop;             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
     for (k=agegomp;k<(agemortsup-3);k++){     fprintf(fichtm,"\
       /*  tpop[k+1]=2;*/   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       tpop[k+1]=tpop[k]-lpop[k];             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("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");     fprintf(fichtm,"\
     for (k=agegomp;k<(agemortsup-2);k++)   - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       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]);             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
         fprintf(fichtm,"\
       - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */     <a href=\"%s\">%s</a> <br>\n",
     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);             estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
         if(prevfcast==1){
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \       fprintf(fichtm,"\
                      stepm, weightopt,\   - Prevalence projections by age and states:                            \
                      model,imx,p,matcov,agemortsup);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
         }
     free_vector(lsurv,1,AGESUP);  
     free_vector(lpop,1,AGESUP);     fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     free_vector(tpop,1,AGESUP);  
   } /* Endof if mle==-3 */     m=pow(2,nqveff);
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   else{ /* For mle >=1 */  
       jj1=0;
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */     for(k1=1; k1<=m;k1++){
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);  
     for (k=1; k<=npar;k++)       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       printf(" %d %8.5f",k,p[k]);       jj1++;
     printf("\n");       if (cptcovn > 0) {
     globpr=1; /* to print the contributions */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */         for (cpt=1; cpt<=nqveff;cpt++){ 
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
     for (k=1; k<=npar;k++)           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
       printf(" %d %8.5f",k,p[k]);         }
     printf("\n");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     if(mle>=1){ /* Could be 1 or 2 */         if(invalidvarcomb[k1]){
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);           fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
     }           printf("\nCombination (%d) ignored because no cases \n",k1); 
               continue;
     /*--------- results files --------------*/         }
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);       }
           /* aij, bij */
           fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       /* Pij */
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       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> \
     for(i=1,jk=1; i <=nlstate; i++){  <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
       for(k=1; k <=(nlstate+ndeath); k++){       /* Quasi-incidences */
         if (k != i) {       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           printf("%d%d ",i,k);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
           fprintf(ficlog,"%d%d ",i,k);   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
           fprintf(ficres,"%1d%1d ",i,k);  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
           for(j=1; j <=ncovmodel; j++){  <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
             printf("%lf ",p[jk]);       /* Survival functions (period) in state j */
             fprintf(ficlog,"%lf ",p[jk]);       for(cpt=1; cpt<=nlstate;cpt++){
             fprintf(ficres,"%lf ",p[jk]);         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> \
             jk++;  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
           }       }
           printf("\n");       /* State specific survival functions (period) */
           fprintf(ficlog,"\n");       for(cpt=1; cpt<=nlstate;cpt++){
           fprintf(ficres,"\n");         fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
         }   Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
       }   <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);
     }       }
     if(mle!=0){       /* Period (stable) prevalence in each health state */
       /* Computing hessian and covariance matrix */       for(cpt=1; cpt<=nlstate;cpt++){
       ftolhess=ftol; /* Usually correct */         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> \
       hesscov(matcov, p, npar, delti, ftolhess, func);  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
     }       }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       if(backcast==1){
     printf("# Scales (for hessian or gradient estimation)\n");         /* Period (stable) back prevalence in each health state */
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");         for(cpt=1; cpt<=nlstate;cpt++){
     for(i=1,jk=1; i <=nlstate; i++){           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> \
       for(j=1; j <=nlstate+ndeath; j++){  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
         if (j!=i) {         }
           fprintf(ficres,"%1d%1d",i,j);       }
           printf("%1d%1d",i,j);       if(prevfcast==1){
           fprintf(ficlog,"%1d%1d",i,j);         /* Projection of prevalence up to period (stable) prevalence in each health state */
           for(k=1; k<=ncovmodel;k++){         for(cpt=1; cpt<=nlstate;cpt++){
             printf(" %.5e",delti[jk]);           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
             fprintf(ficlog," %.5e",delti[jk]);  <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
             fprintf(ficres," %.5e",delti[jk]);         }
             jk++;       }
           }           
           printf("\n");       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficlog,"\n");         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> \
           fprintf(ficres,"\n");  <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 *\/ */
     }     }/* End k1 */
         fprintf(fichtm,"</ul>");
     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)     fprintf(fichtm,"\
       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");  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\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");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
     /* # 121 Var(a12)\n\ */   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
     /* # 122 Cov(b12,a12) Var(b12)\n\ */  But because parameters are usually highly correlated (a higher incidence of disability \
     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */  and a higher incidence of recovery can give very close observed transition) it might \
     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */  be very useful to look not only at linear confidence intervals estimated from the \
     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */  variances but at the covariance matrix. And instead of looking at the estimated coefficients \
     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */  (parameters) of the logistic regression, it might be more meaningful to visualize the \
     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */  covariance matrix of the one-step probabilities. \
     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
      
         fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     /* Just to have a covariance matrix which will be more understandable             subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
        even is we still don't want to manage dictionary of variables     fprintf(fichtm,"\
     */   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     for(itimes=1;itimes<=2;itimes++){             subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
       jj=0;  
       for(i=1; i <=nlstate; i++){     fprintf(fichtm,"\
         for(j=1; j <=nlstate+ndeath; j++){   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           if(j==i) continue;             subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
           for(k=1; k<=ncovmodel;k++){     fprintf(fichtm,"\
             jj++;   - 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): \
             ca[0]= k+'a'-1;ca[1]='\0';     <a href=\"%s\">%s</a> <br>\n</li>",
             if(itimes==1){             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
               if(mle>=1)     fprintf(fichtm,"\
                 printf("#%1d%1d%d",i,j,k);   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
               fprintf(ficlog,"#%1d%1d%d",i,j,k);     <a href=\"%s\">%s</a> <br>\n</li>",
               fprintf(ficres,"#%1d%1d%d",i,j,k);             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
             }else{     fprintf(fichtm,"\
               if(mle>=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",
                 printf("%1d%1d%d",i,j,k);             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
               fprintf(ficlog,"%1d%1d%d",i,j,k);     fprintf(fichtm,"\
               fprintf(ficres,"%1d%1d%d",i,j,k);   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
             }             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
             ll=0;     fprintf(fichtm,"\
             for(li=1;li <=nlstate; li++){   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
               for(lj=1;lj <=nlstate+ndeath; lj++){             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
                 if(lj==li) continue;  
                 for(lk=1;lk<=ncovmodel;lk++){  /*  if(popforecast==1) fprintf(fichtm,"\n */
                   ll++;  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   if(ll<=jj){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                     cb[0]= lk +'a'-1;cb[1]='\0';  /*      <br>",fileres,fileres,fileres,fileres); */
                     if(ll<jj){  /*  else  */
                       if(itimes==1){  /*    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); */
                         if(mle>=1)     fflush(fichtm);
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
                         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);     m=pow(2,nqveff);
                       }else{     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                         if(mle>=1)  
                           printf(" %.5e",matcov[jj][ll]);     jj1=0;
                         fprintf(ficlog," %.5e",matcov[jj][ll]);     for(k1=1; k1<=m;k1++){
                         fprintf(ficres," %.5e",matcov[jj][ll]);       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                       }       jj1++;
                     }else{       if (cptcovn > 0) {
                       if(itimes==1){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                         if(mle>=1)         for (cpt=1; cpt<=nqveff;cpt++) 
                           printf(" Var(%s%1d%1d)",ca,i,j);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);  
                       }else{         if(invalidvarcomb[k1]){
                         if(mle>=1)           fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
                           printf(" %.5e",matcov[jj][ll]);           continue;
                         fprintf(ficlog," %.5e",matcov[jj][ll]);         }
                         fprintf(ficres," %.5e",matcov[jj][ll]);       }
                       }       for(cpt=1; cpt<=nlstate;cpt++) {
                     }         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>\
                 } /* end lk */  <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
               } /* end lj */       }
             } /* end li */       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
             if(mle>=1)  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
               printf("\n");  true period expectancies (those weighted with period prevalences are also\
             fprintf(ficlog,"\n");   drawn in addition to the population based expectancies computed using\
             fprintf(ficres,"\n");   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
             numlinepar++;  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
           } /* end k*/       /* } /\* end i1 *\/ */
         } /*end j */     }/* End k1 */
       } /* end i */     fprintf(fichtm,"</ul>");
     } /* end itimes */     fflush(fichtm);
      }
     fflush(ficlog);  
     fflush(ficres);  /******************* Gnuplot file **************/
      void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);    char dirfileres[132],optfileres[132];
       fgets(line, MAXLINE, ficpar);    char gplotcondition[132];
       puts(line);    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
       fputs(line,ficparo);    int lv=0, vlv=0, kl=0;
     }    int ng=0;
     ungetc(c,ficpar);    int vpopbased;
        int ioffset; /* variable offset for columns */
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     if (estepm==0 || estepm < stepm) estepm=stepm;  /*     printf("Problem with file %s",optionfilegnuplot); */
     if (fage <= 2) {  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       bage = ageminpar;  /*   } */
       fage = agemaxpar;  
     }    /*#ifdef windows */
        fprintf(ficgp,"cd \"%s\" \n",pathc);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /*#endif */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    m=pow(2,nqveff);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
        /* Contribution to likelihood */
     while((c=getc(ficpar))=='#' && c!= EOF){    /* Plot the probability implied in the likelihood */
       ungetc(c,ficpar);    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
       fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
       puts(line);    /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
       fputs(line,ficparo);    fprintf(ficgp,"\nset ter pngcairo size 640, 480");
     }  /* nice for mle=4 plot by number of matrix products.
     ungetc(c,ficpar);     replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
      /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     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(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     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(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    fprintf(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));
     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,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     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,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
        for (i=1; i<= nlstate ; i ++) {
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       ungetc(c,ficpar);      fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fgets(line, MAXLINE, ficpar);      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);
       puts(line);      for (j=2; j<= nlstate+ndeath ; j ++) {
       fputs(line,ficparo);        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);
     }      }
     ungetc(c,ficpar);      fprintf(ficgp,";\nset out; unset ylabel;\n"); 
        }
        /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;    /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;    /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
        fprintf(ficgp,"\nset out;unset log\n");
     fscanf(ficpar,"pop_based=%d\n",&popbased);    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficparo,"pop_based=%d\n",popbased);    
     fprintf(ficres,"pop_based=%d\n",popbased);      strcpy(dirfileres,optionfilefiname);
        strcpy(optfileres,"vpl");
     while((c=getc(ficpar))=='#' && c!= EOF){    /* 1eme*/
       ungetc(c,ficpar);    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
       fgets(line, MAXLINE, ficpar);      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
       puts(line);        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       fputs(line,ficparo);        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
     }        for (k=1; k<=nqveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
     ungetc(c,ficpar);          lv= decodtabm(k1,k,nqveff); /* Should be the value of the covariate corresponding to k1 combination */
              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
     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);          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
     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);          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
     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);          vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
     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);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
     /* day and month of proj2 are not used but only year anproj2.*/        }
            fprintf(ficgp,"\n#\n");
            if(invalidvarcomb[k1]){
              fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/          continue;
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        }
      
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);        fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
            fprintf(ficgp,"set xlabel \"Age\" \n\
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\  set ylabel \"Probability\" \n   \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\  set ter svg size 640, 480\n     \
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
                                
    /*------------ free_vector  -------------*/        for (i=1; i<= nlstate ; i ++) {
    /*  chdir(path); */          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
            else        fprintf(ficgp," %%*lf (%%*lf)");
     free_ivector(wav,1,imx);        }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        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);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);        for (i=1; i<= nlstate ; i ++) {
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
     free_lvector(num,1,n);          else fprintf(ficgp," %%*lf (%%*lf)");
     free_vector(agedc,1,n);        } 
     /*free_matrix(covar,0,NCOVMAX,1,n);*/        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        for (i=1; i<= nlstate ; i ++) {
     fclose(ficparo);          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
     fclose(ficres);          else fprintf(ficgp," %%*lf (%%*lf)");
         }  
         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/        if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
     strcpy(filerespl,"pl");          fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
     strcat(filerespl,fileres);          if(nqveff ==0){
     if((ficrespl=fopen(filerespl,"w"))==NULL) {            fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;          }else{
       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;            kl=0;
     }            for (k=1; k<=nqveff; k++){    /* For each combination of covariate  */
     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);              lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
     pstamp(ficrespl);              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
     fprintf(ficrespl,"# Period (stable) prevalence \n");              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
     fprintf(ficrespl,"#Age ");              vlv= nbcode[Tvaraff[k]][lv];
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              kl++;
     fprintf(ficrespl,"\n");              /* 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 */ 
     prlim=matrix(1,nlstate,1,nlstate);              /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/
     agebase=ageminpar;              if(k==nqveff){
     agelim=agemaxpar;                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
     ftolpl=1.e-10;                        6+(cpt-1),  cpt );
     i1=cptcoveff;              }else{
     if (cptcovn < 1){i1=1;}                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){              }
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            } /* end covariate */
         k=k+1;          } /* end if no covariate */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        } /* end if backcast */
         fprintf(ficrespl,"\n#******");        fprintf(ficgp,"\nset out \n");
         printf("\n#******");      } /* k1 */
         fprintf(ficlog,"\n#******");    } /* cpt */
         for(j=1;j<=cptcoveff;j++) {    /*2 eme*/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k1=1; k1<= m ; k1 ++) { 
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
         }      for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
         fprintf(ficrespl,"******\n");        lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
         printf("******\n");        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         fprintf(ficlog,"******\n");        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         for (age=agebase; age<=agelim; age++){        vlv= nbcode[Tvaraff[k]][lv];
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           fprintf(ficrespl,"%.0f ",age );      }
           for(j=1;j<=cptcoveff;j++)      fprintf(ficgp,"\n#\n");
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if(invalidvarcomb[k1]){
           for(i=1; i<=nlstate;i++)        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             fprintf(ficrespl," %.5f", prlim[i][i]);        continue;
           fprintf(ficrespl,"\n");      }
         }                          
       }      fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
     }      for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
     fclose(ficrespl);        if(vpopbased==0)
           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
     /*------------- h Pij x at various ages ------------*/        else
            fprintf(ficgp,"\nreplot ");
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);        for (i=1; i<= nlstate+1 ; i ++) {
     if((ficrespij=fopen(filerespij,"w"))==NULL) {          k=2*i;
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          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);
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;          for (j=1; j<= nlstate+1 ; j ++) {
     }            if (j==i) fprintf(ficgp," %%lf (%%lf)");
     printf("Computing pij: result on file '%s' \n", filerespij);            else fprintf(ficgp," %%*lf (%%*lf)");
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);          }   
            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
     stepsize=(int) (stepm+YEARM-1)/YEARM;          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
     /*if (stepm<=24) stepsize=2;*/          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {
     agelim=AGESUP;            if (j==i) fprintf(ficgp," %%lf (%%lf)");
     hstepm=stepsize*YEARM; /* Every year of age */            else fprintf(ficgp," %%*lf (%%*lf)");
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          }   
           fprintf(ficgp,"\" t\"\" w l lt 0,");
     /* hstepm=1;   aff par mois*/          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);
     pstamp(ficrespij);          for (j=1; j<= nlstate+1 ; j ++) {
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){            else fprintf(ficgp," %%*lf (%%*lf)");
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }   
         k=k+1;          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         fprintf(ficrespij,"\n#****** ");          else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         for(j=1;j<=cptcoveff;j++)        } /* state */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* vpopbased */
         fprintf(ficrespij,"******\n");      fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
            } /* k1 */
         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 */    /*3eme*/
     for (k1=1; k1<= m ; k1 ++) { 
           /*      nhstepm=nhstepm*YEARM; aff par mois*/  
       for (cpt=1; cpt<= nlstate ; cpt ++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
           oldm=oldms;savm=savms;        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");          /* 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 */
               fprintf(ficrespij," %1d-%1d",i,j);          vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficrespij,"\n");          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           for (h=0; h<=nhstepm; h++){        }
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fprintf(ficgp,"\n#\n");
             for(i=1; i<=nlstate;i++)        if(invalidvarcomb[k1]){
               for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          continue;
             fprintf(ficrespij,"\n");        }
           }                          
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*       k=2+nlstate*(2*cpt-2); */
           fprintf(ficrespij,"\n");        k=2+(nlstate+1)*(cpt-1);
         }        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       }        fprintf(ficgp,"set ter svg size 640, 480\n\
     }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fclose(ficrespij);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     for(i=1;i<=AGESUP;i++)                                  
       for(j=1;j<=NCOVMAX;j++)        */
         for(k=1;k<=NCOVMAX;k++)        for (i=1; i< nlstate ; i ++) {
           probs[i][j][k]=0.;          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
     /*---------- Forecasting ------------------*/                                  
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/        } 
     if(prevfcast==1){        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
       /*    if(stepm ==1){*/      }
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);    }
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/    
       /*      }  */    /* 4eme */
       /*      else{ */    /* Survival functions (period) from state i in state j by initial state i */
       /*        erreur=108; */    for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       /*        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); */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       /*      } */        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
     }        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
            lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
     /*---------- Health expectancies and variances ------------*/          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
     strcpy(filerest,"t");          vlv= nbcode[Tvaraff[k]][lv];
     strcat(filerest,fileres);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
     if((ficrest=fopen(filerest,"w"))==NULL) {        }
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficgp,"\n#\n");
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        if(invalidvarcomb[k1]){
     }          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);          continue;
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);        }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
     strcpy(filerese,"e");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
     strcat(filerese,fileres);  set ter svg size 640, 480\n                                                                                                                                                                                     \
     if((ficreseij=fopen(filerese,"w"))==NULL) {  unset log y\n                                                                                                                                                                                                                                           \
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        k=3;
     }        for (i=1; i<= nlstate ; i ++){
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);          if(i==1){
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           }else{
     strcpy(fileresstde,"stde");            fprintf(ficgp,", '' ");
     strcat(fileresstde,fileres);          }
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {          l=(nlstate+ndeath)*(i-1)+1;
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);          for (j=2; j<= nlstate+ndeath ; j ++)
     }            fprintf(ficgp,"+$%d",k+l+j-1);
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);        } /* nlstate */
         fprintf(ficgp,"\nset out\n");
     strcpy(filerescve,"cve");      } /* end cpt state*/ 
     strcat(filerescve,fileres);    } /* end covariate */  
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {          
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);  /* 5eme */
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);    /* Survival functions (period) from state i in state j by final state j */
     }    for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);                          
         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);
     strcpy(fileresv,"v");        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
     strcat(fileresv,fileres);                                  lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
     if((ficresvij=fopen(fileresv,"w"))==NULL) {                                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);                                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
     }                                  vlv= nbcode[Tvaraff[k]][lv];
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }
         fprintf(ficgp,"\n#\n");
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */        if(invalidvarcomb[k1]){
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);                                  fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
     /*  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",\                                  continue;
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);        }
     */                          
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
     if (mobilav!=0) {        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  set ter svg size 640, 480\n                                                                                                                                                                                     \
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  unset log y\n                                                                                                                                                                                                                                           \
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);        k=3;
       }        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
     }                                  if(j==1)
                                           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){                                  else
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                          fprintf(ficgp,", '' ");
         k=k+1;                                  l=(nlstate+ndeath)*(cpt-1) +j;
         fprintf(ficrest,"\n#****** ");                                  fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
         for(j=1;j<=cptcoveff;j++)                                  /* for (i=2; i<= nlstate+ndeath ; i ++) */
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  /*   fprintf(ficgp,"+$%d",k+l+i-1); */
         fprintf(ficrest,"******\n");                                  fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficreseij,"\n#****** ");        fprintf(ficgp,", '' ");
         fprintf(ficresstdeij,"\n#****** ");        fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         fprintf(ficrescveij,"\n#****** ");        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
         for(j=1;j<=cptcoveff;j++) {                                  l=(nlstate+ndeath)*(cpt-1) +j;
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  if(j < nlstate)
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                          fprintf(ficgp,"$%d +",k+l);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  else
         }                                          fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         fprintf(ficreseij,"******\n");        }
         fprintf(ficresstdeij,"******\n");        fprintf(ficgp,"\nset out\n");
         fprintf(ficrescveij,"******\n");      } /* end cpt state*/ 
     } /* end covariate */  
         fprintf(ficresvij,"\n#****** ");          
         for(j=1;j<=cptcoveff;j++)  /* 6eme */
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* CV preval stable (period) for each covariate */
         fprintf(ficresvij,"******\n");    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 */
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                          
         oldm=oldms;savm=savms;        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);          for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);                                    lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                    /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
         oldm=oldms;savm=savms;                                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);                                  vlv= nbcode[Tvaraff[k]][lv];
         if(popbased==1){                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           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,"\n#\n");
         if(invalidvarcomb[k1]){
         pstamp(ficrest);                                  fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");                                  continue;
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        }
         fprintf(ficrest,"\n");                          
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
         epj=vector(1,nlstate+1);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
         for(age=bage; age <=fage ;age++){  set ter svg size 640, 480\n                                                                                                                                                                              \
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  unset log y\n                                                                                                                                                                                                                                    \
           if (popbased==1) {  plot [%.f:%.f]  ", ageminpar, agemaxpar);
             if(mobilav ==0){        k=3; /* Offset */
               for(i=1; i<=nlstate;i++)        for (i=1; i<= nlstate ; i ++){
                 prlim[i][i]=probs[(int)age][i][k];                                  if(i==1)
             }else{ /* mobilav */                                          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
               for(i=1; i<=nlstate;i++)                                  else
                 prlim[i][i]=mobaverage[(int)age][i][k];                                          fprintf(ficgp,", '' ");
             }                                  l=(nlstate+ndeath)*(i-1)+1;
           }                                  fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                                          for (j=2; j<= nlstate ; j ++)
           fprintf(ficrest," %4.0f",age);                                          fprintf(ficgp,"+$%d",k+l+j-1);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                  fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
             for(i=1, epj[j]=0.;i <=nlstate;i++) {        } /* nlstate */
               epj[j] += prlim[i][i]*eij[i][j][(int)age];        fprintf(ficgp,"\nset out\n");
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      } /* end cpt state*/ 
             }    } /* end covariate */  
             epj[nlstate+1] +=epj[j];          
           }          
   /* 7eme */
           for(i=1, vepp=0.;i <=nlstate;i++)    if(backcast == 1){
             for(j=1;j <=nlstate;j++)      /* CV back preval stable (period) for each covariate */
               vepp += vareij[i][j][(int)age];      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           for(j=1;j <=nlstate;j++){                                  fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                                  for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
           }                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
           fprintf(ficrest,"\n");                                          /* 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 */
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                          vlv= nbcode[Tvaraff[k]][lv];
         free_vector(epj,1,nlstate+1);                                          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }                                  }
     }                                  fprintf(ficgp,"\n#\n");
     free_vector(weight,1,n);                                  if(invalidvarcomb[k1]){
     free_imatrix(Tvard,1,15,1,2);                                          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
     free_imatrix(s,1,maxwav+1,1,n);                                          continue;
     free_matrix(anint,1,maxwav,1,n);                                  }
     free_matrix(mint,1,maxwav,1,n);                                  
     free_ivector(cod,1,n);                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
     free_ivector(tab,1,NCOVMAX);                                  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     fclose(ficreseij);  set ter svg size 640, 480\n                                                                                                                                                                                     \
     fclose(ficresstdeij);  unset log y\n                                                                                                                                                                                                                                           \
     fclose(ficrescveij);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
     fclose(ficresvij);                                  k=3; /* Offset */
     fclose(ficrest);                                  for (i=1; i<= nlstate ; i ++){
     fclose(ficpar);                                          if(i==1)
                                                    fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
     /*------- Variance of period (stable) prevalence------*/                                            else
                                                   fprintf(ficgp,", '' ");
     strcpy(fileresvpl,"vpl");                                          /* l=(nlstate+ndeath)*(i-1)+1; */
     strcat(fileresvpl,fileres);                                          l=(nlstate+ndeath)*(cpt-1)+1;
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                                          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);                                          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
       exit(0);                                          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
     }                                          /* for (j=2; j<= nlstate ; j ++) */
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);                                          /*      fprintf(ficgp,"+$%d",k+l+j-1); */
                                           /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){                                          fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                  } /* nlstate */
         k=k+1;                                  fprintf(ficgp,"\nset out\n");
         fprintf(ficresvpl,"\n#****** ");        } /* end cpt state*/ 
         for(j=1;j<=cptcoveff;j++)      } /* end covariate */  
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    } /* End if backcast */
         fprintf(ficresvpl,"******\n");    
          /* 8eme */
         varpl=matrix(1,nlstate,(int) bage, (int) fage);    if(prevfcast==1){
         oldm=oldms;savm=savms;      /* Projection from cross-sectional to stable (period) for each covariate */
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);      
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       }        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
     }                                  fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                   for (k=1; k<=nqveff; k++){    /* For each correspondig covariate value  */
     fclose(ficresvpl);                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
     /*---------- End : free ----------------*/                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                                          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);                                          vlv= nbcode[Tvaraff[k]][lv];
                                           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
   }  /* mle==-3 arrives here for freeing */                                  }
   free_matrix(prlim,1,nlstate,1,nlstate);                                  fprintf(ficgp,"\n#\n");
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                                  if(invalidvarcomb[k1]){
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                                          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                                          continue;
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                                  }
     free_matrix(covar,0,NCOVMAX,1,n);                                  
     free_matrix(matcov,1,npar,1,npar);                                  fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
     /*free_vector(delti,1,npar);*/                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                                  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
     free_matrix(agev,1,maxwav,1,imx);  set ter svg size 640, 480\n                                                                                                                                                                                     \
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  unset log y\n                                                                                                                                                                                                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
     free_ivector(ncodemax,1,8);                                  for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
     free_ivector(Tvar,1,15);                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
     free_ivector(Tprod,1,15);                                          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
     free_ivector(Tvaraff,1,15);                                          /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
     free_ivector(Tage,1,15);                                          /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
     free_ivector(Tcode,1,100);                                          if(i==1){
                                                   fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);                                          }else{
     free_imatrix(codtab,1,100,1,10);                                                  fprintf(ficgp,",\\\n '' ");
   fflush(fichtm);                                          }
   fflush(ficgp);                                          if(nqveff ==0){ /* No covariate */
                                                    ioffset=2; /* Age is in 2 */
                                                   /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
   if((nberr >0) || (nbwarn>0)){                                                  /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);                                                  /*# 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,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);                                                  /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
   }else{                                                  fprintf(ficgp," u %d:(", ioffset); 
     printf("End of Imach\n");                                                  if(i==nlstate+1)
     fprintf(ficlog,"End of Imach\n");                                                          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 );
   printf("See log file on %s\n",filelog);                                                  else
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                                                          fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
   (void) gettimeofday(&end_time,&tzp);                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
   tm = *localtime(&end_time.tv_sec);                                          }else{ /* more than 2 covariates */
   tmg = *gmtime(&end_time.tv_sec);                                                  if(nqveff ==1){
   strcpy(strtend,asctime(&tm));                                                          ioffset=4; /* Age is in 4 */
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);                                                  }else{
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);                                                          ioffset=6; /* Age is in 6 */
   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));                                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);                                                  }   
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));                                                  fprintf(ficgp," u %d:(",ioffset); 
   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);                                                  kl=0;
   /*  printf("Total time was %d uSec.\n", total_usecs);*/                                                  strcpy(gplotcondition,"(");
 /*   if(fileappend(fichtm,optionfilehtm)){ */                                                  for (k=1; k<=nqveff; k++){    /* For each covariate writing the chain of conditions */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);                                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
   fclose(fichtm);                                                          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);                                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
   fclose(fichtmcov);                                                          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
   fclose(ficgp);                                                          vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
   fclose(ficlog);                                                          kl++;
   /*------ End -----------*/                                                          sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                           kl++;
                                                           if(k <nqveff && nqveff>1)
    printf("Before Current directory %s!\n",pathcd);                                                                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
    if(chdir(pathcd) != 0)                                                  }
     printf("Can't move to directory %s!\n",path);                                                  strcpy(gplotcondition+strlen(gplotcondition),")");
   if(getcwd(pathcd,MAXLINE) > 0)                                                  /* 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 *\/ */
     printf("Current directory %s!\n",pathcd);                                                  /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
   /*strcat(plotcmd,CHARSEPARATOR);*/                                                  /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
   sprintf(plotcmd,"gnuplot");                                                  /* ''  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*/
 #ifndef UNIX                                                  if(i==nlstate+1){
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
 #endif                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
   if(!stat(plotcmd,&info)){                                                  }else{
     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
     if(!stat(getenv("GNUPLOTBIN"),&info)){                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);                                                  }
     }else                                          } /* end if covariate */
       strcpy(pplotcmd,plotcmd);                                  } /* nlstate */
 #ifdef UNIX                                  fprintf(ficgp,"\nset out\n");
     strcpy(plotcmd,GNUPLOTPROGRAM);        } /* end cpt state*/
     if(!stat(plotcmd,&info)){      } /* end covariate */
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);    } /* End if prevfcast */
     }else          
       strcpy(pplotcmd,plotcmd);          
 #endif    /* proba elementaires */
   }else    fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     strcpy(pplotcmd,plotcmd);    for(i=1,jk=1; i <=nlstate; i++){
        fprintf(ficgp,"# initial state %d\n",i);
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);      for(k=1; k <=(nlstate+ndeath); k++){
   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);        if (k != i) {
                                   fprintf(ficgp,"#   current state %d\n",k);
   if((outcmd=system(plotcmd)) != 0){                                  for(j=1; j <=ncovmodel; j++){
     printf("\n Problem with gnuplot\n");                                          fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
   }                                          jk++; 
   printf(" Wait...");                                  }
   while (z[0] != 'q') {                                  fprintf(ficgp,"\n");
     /* chdir(path); */        }
     printf("\nType e to edit output files, g to graph again and q for exiting: ");      }
     scanf("%s",z);    }
 /*     if (z[0] == 'c') system("./imach"); */    fprintf(ficgp,"##############\n#\n");
     if (z[0] == 'e') {          
       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);    /*goto avoid;*/
       system(optionfilehtm);    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");
     else if (z[0] == 'g') system(plotcmd);    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     else if (z[0] == 'q') exit(0);    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
   }    fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
   end:    fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
   while (z[0] != 'q') {    fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     printf("\nType  q for exiting: ");    fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     scanf("%s",z);    fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
   }    fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
 }    fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
     for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
       fprintf(ficgp,"# ng=%d\n",ng);
       fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",nqveff,m);
       for(jk=1; jk <=m; jk++) {
         fprintf(ficgp,"#    jk=%d\n",jk);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
         fprintf(ficgp,"\nset ter svg size 640, 480 ");
         if (ng==1){
           fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
           fprintf(ficgp,"\nunset log y");
         }else if (ng==2){
           fprintf(ficgp,"\nset ylabel \"Probability\"\n");
           fprintf(ficgp,"\nset log y");
         }else if (ng==3){
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           fprintf(ficgp,"\nset log y");
         }else
           fprintf(ficgp,"\nunset title ");
         fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
           for(k=1; k<=(nlstate+ndeath); k++) {
             if (k != k2){
               switch( ng) {
               case 1:
                 if(nagesqr==0)
                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 2: /* ng=2 */
                 if(nagesqr==0)
                   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 3:
                 if(nagesqr==0)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                 break;
               }
               ij=1;/* To be checked else nbcode[0][0] wrong */
               for(j=3; j <=ncovmodel-nagesqr; j++) {
                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                 if(ij <=cptcovage) { /* Bug valgrind */
                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                     ij++;
                   }
                 }
                 else
                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
               }
             }else{
               i=i-ncovmodel;
               if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                 fprintf(ficgp," (1.");
             }
              
             if(ng != 1){
               fprintf(ficgp,")/(1");
                
               for(k1=1; k1 <=nlstate; k1++){ 
                 if(nagesqr==0)
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                  
                 ij=1;
                 for(j=3; j <=ncovmodel-nagesqr; j++){
                   if(ij <=cptcovage) { /* Bug valgrind */
                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                       /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                       ij++;
                     }
                   }
                   else
                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                 }
                 fprintf(ficgp,")");
               }
               fprintf(ficgp,")");
               if(ng ==2)
                 fprintf(ficgp," t \"p%d%d\" ", k2,k);
               else /* ng= 3 */
                 fprintf(ficgp," t \"i%d%d\" ", k2,k);
             }else{ /* end ng <> 1 */
               if( k !=k2) /* logit p11 is hard to draw */
                 fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
             }
             if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
               fprintf(ficgp,",");
             if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
               fprintf(ficgp,",");
             i=i+ncovmodel;
           } /* end k */
         } /* end k2 */
         fprintf(ficgp,"\n set out\n");
       } /* end jk */
     } /* end ng */
     /* avoid: */
     fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
    int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
      
      int i, cpt, cptcod;
      int modcovmax =1;
      int mobilavrange, mob;
      int iage=0;
   
      double sum=0.;
      double age;
      double *sumnewp, *sumnewm;
      double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     
     
      /* modcovmax=2*nqveff;/\* Max number of modalities. We suppose  */
      /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
   
      sumnewp = vector(1,ncovcombmax);
      sumnewm = vector(1,ncovcombmax);
      agemingood = vector(1,ncovcombmax);  
      agemaxgood = vector(1,ncovcombmax);
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        sumnewm[cptcod]=0.;
        sumnewp[cptcod]=0.;
        agemingood[cptcod]=0;
        agemaxgood[cptcod]=0;
      }
      if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
     
      if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
        */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                }
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
            }
          }/* end age */
        }/* end mob */
      }else
        return -1;
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
        if(invalidvarcomb[cptcod]){
          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
          continue;
        }
   
        agemingood[cptcod]=fage-(mob-1)/2;
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemingood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        /* From youngest, finding the oldest wrong */
        agemaxgood[cptcod]=bage+(mob-1)/2;
        for (age=bage+(mob-1)/2; age<=fage; age++){
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
                   
        for (age=bage; age<=fage; age++){
          printf("%d %d ", cptcod, (int)age);
          sumnewp[cptcod]=0.;
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewp[cptcod]+=probs[(int)age][i][cptcod];
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
          }
          /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
        }
        /* printf("\n"); */
        /* } */
        /* brutal averaging */
        for (i=1; i<=nlstate;i++){
          for (age=1; age<=bage; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }        
          for (age=fage; age<=AGESUP; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }
        } /* end i status */
        for (i=nlstate+1; i<=nlstate+ndeath;i++){
          for (age=1; age<=AGESUP; age++){
            /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
            mobaverage[(int)age][i][cptcod]=0.;
          }
        }
      }/* end cptcod */
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
    
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int nqveff){
     /* 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 (nqveff==0) ncodemax[nqveff]=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=nqveff;
     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[nqveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
         for(j=1;j<=nqveff;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<=nqveff;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 nqveff){ */
   /*   /\* 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 (nqveff==0) ncodemax[nqveff]=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=nqveff; */
   /*   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[nqveff];cptcod++){ */
   /*       k=k+1; */
   /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
   /*       for(j=1;j<=nqveff;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<=nqveff;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 (nqveff==0) ncodemax[nqveff]=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[nqveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=nqveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   /*fprintf(ficrespop," %.3f", kk1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                 for(j=1; j<=nlstate;j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                 }
                 tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
               
               if (h==(int)(calagedatem+12*cpt))
                 for(j=1; j<=nlstate;j++) 
                   fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
         
         /******/
         
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       } 
     }
     
     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
    
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=1;i<=imx ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0, iv=0;
     int lstra;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
   
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
       
       /* Loops on waves */
       for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           /* what_kind_of_number(strb); */
                                           dval=strtod(strb,&endptr); 
                                           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
                                           /* if(strb != endptr && *endptr == '\0') */
                                           /*    dval=dlval; */
                                           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                           cotqvar[j][iv][i]=dval; 
                                   }
                                   strcpy(line,stra);
         }/* end loop ntqv */
                           
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           lval=strtol(strb,&endptr,10); 
                                           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                   }
                                   if(lval <-1 || lval >1){
                                           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                                                                                                                \
    Exiting.\n",lval,linei, i,line,j);
                                           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                                           return 1;
                                   }
                                   cotvar[j][iv][i]=(double)(lval);
                                   strcpy(line,stra);
         }/* end loop ntv */
   
         /* Statuses  at wave */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
                                   lval=-1;
         }else{
                                   errno=0;
                                   lval=strtol(strb,&endptr,10); 
                                   /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                                   if( strb[0]=='\0' || (*endptr != '\0')){
                                           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
                                           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
                                           return 1;
                                   }
         }
        
         s[j][i]=lval;
   
         /* Date of Interview */
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
                                   month=99;
                                   year=9999;
         }else{
                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
                                   return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* End loop on waves */
   
       /* Date of death */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
                           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
                           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       /* Date of birth */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
                           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
                           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
   
       /* Sample weight */
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
   
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
                                   lval=-1;
         }else{
                                   errno=0;
                                   /* what_kind_of_number(strb); */
                                   dval=strtod(strb,&endptr);
                                   /* if(strb != endptr && *endptr == '\0') */
                                   /*   dval=dlval; */
                                   /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                   if( strb[0]=='\0' || (*endptr != '\0')){
                                           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
                                           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
                                           return 1;
                                   }
                                   coqvar[iv][i]=dval; 
         }
         strcpy(line,stra);
       }/* end loop nqv */
       
       /* Covariate values */
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing covariate value */
                                   lval=-1;
         }else{
                                   errno=0;
                                   lval=strtol(strb,&endptr,10); 
                                   if( strb[0]=='\0' || (*endptr != '\0')){
                                           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
                                           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
                                           return 1;
                                   }
         }
         if(lval <-1 || lval >1){
                                   printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
                                   fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                                   return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
           printf("Exiting readdata: ");
           fclose(fic);
           return (1);
   }
   
   void removespace(char *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 =5-3=2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                                                                                    * cst, age and age*age 
                                                                                    * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                           /* including age products which are counted in cptcovage.
                            * but the covariates which are products must be treated 
                            * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
       
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
   
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           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);*/
   /* Dispatching in quantitative and time varying covariates */
   
           for(k=1, ncoveff=0, nqveff=0, ntveff=0, nqtveff=0;k<=cptcovn; k++){ /* or cptocvt */
                   if (Tvar[k] <=ncovcol){
                           ncoveff++;
                   }else if( Tvar[k] <=ncovcol+nqv){
                           nqveff++;
                   }else if( Tvar[k] <=ncovcol+nqv+ntv){
                           ntveff++;
                   }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
                           nqtveff++;
                   }else
                           printf("Error in effective covariates \n");
           }
   
     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
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\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,ncoveff);
     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<=nqveff;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<=nqveff;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<=nqveff;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,nqveff);
     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<=nqveff;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<=nqveff;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<=nqveff;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,nqveff);
                   /* 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,nqveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=nqveff;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,nqveff);
     /* 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,nqveff); k++){
       fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=nqveff;j++)
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
         
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
           fprintf(ficrespijb,"\n");
         }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       }
       /*}*/
     }
     return 0;
    } /*  hBijx */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
     int ncvyear=0; /* Number of years needed for the period prevalence to converge */
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb=0.;
   
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
     double fret;
     double dum=0.; /* Dummy variable */
     double ***p3mat;
     /* double ***mobaverage; */
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt, c2;
     int jl=0;
     int i1, j1, jk, stepsize=0;
     int count=0;
   
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110., age, agelim=0., agebase=0.;
     double ftolpl=FTOL;
     double **prlim;
     double **bprlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
   
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
     syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       if(!fgets(pathr,FILENAMELENGTH,stdin)){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
       }
       i=strlen(pathr);
       if( i==0 ){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"Version %s %s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo(1);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
     strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileresu);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   
       /* First parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
       numlinepar++;
       printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     }
     /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 11) {
         printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
       }
       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
     /* Third parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
       if (num_filled == 0)
               model[0]='\0';
       else if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
           strcpy(model,modeltemp); 
         }
       }
       /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
       printf("model=1+age+%s\n",model);fflush(stdout);
     }
     /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     coqvar=matrix(1,nqv,1,n);  /**< used in readdata */
     cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< used in readdata */
     cotqvar=ma3x(1,maxwav,1,nqtv,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
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     /* free_vector(moisdc,1,n); */
     /* free_vector(andc,1,n); */
     /* */
     
     wav=ivector(1,imx);
     /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
     /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
     /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
     dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
     bh=imatrix(1,lastpass-firstpass+2,1,imx);
     mw=imatrix(1,lastpass-firstpass+2,1,imx);
      
     /* Concatenates waves */
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     */
   
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
           cptcoveff=0;
     if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
       tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
           }
           
           ncovcombmax=pow(2,cptcoveff);
           invalidvarcomb=ivector(1, ncovcombmax); 
           for(i=1;i<ncovcombmax;i++)
                   invalidvarcomb[i]=0;
   
     /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
   
     /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
      * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
      * (currently 0 or 1) in the data.
      * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
      * corresponding modality (h,j).
      */
   
     h=0;
     /*if (cptcovn > 0) */
     m=pow(2,cptcoveff);
    
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to m=2**k
              * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
              * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     2
              *    10     2     1     1     2
              *    11 i=6 1     2     1     2
              *    12     2     2     1     2
              *    13 i=7 1 i=4 1     2     2    
              *    14     2     1     2     2
              *    15 i=8 1     2     2     2
              *    16     2     2     2     2
              */
     /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
        /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
        * and the value of each covariate?
        * V1=1, V2=1, V3=2, V4=1 ?
        * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
        * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
        * In order to get the real value in the data, we use nbcode
        * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
        * We are keeping this crazy system in order to be able (in the future?) 
        * to have more than 2 values (0 or 1) for a covariate.
        * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
        * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
        *              bbbbbbbb
        *              76543210     
        *   h-1        00000101 (6-1=5)
        *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
        *           &
        *     1        00000001 (1)
        *              00000000        = 1 & ((h-1) >> (k-1))
        *          +1= 00000001 =1 
        *
        * h=14, k=3 => h'=h-1=13, k'=k-1=2
        *          h'      1101 =2^3+2^2+0x2^1+2^0
        *    >>k'            11
        *          &   00000001
        *            = 00000001
        *      +1    = 00000010=2    =  codtabm(14,3)   
        * Reverse h=6 and m=16?
        * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
        * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
        * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
        * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
        * V3=decodtabm(14,3,2**4)=2
        *          h'=13   1101 =2^3+2^2+0x2^1+2^0
        *(h-1) >> (j-1)    0011 =13 >> 2
        *          &1 000000001
        *           = 000000001
        *         +1= 000000010 =2
        *                  2211
        *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
        *                  V3=2
                    * codtabm and decodtabm are identical
        */
   
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-MORT_");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-MORT_");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   <font size=\"2\">IMaCh-%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
                                                           firstpass, lastpass,  stepm,  weightopt, model);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
                   for(i=1;i<=NDIM;i++)
                           for(j=1;j<=NDIM;j++)
                                   ximort[i][j]=0.;
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
                   
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
                                   if (s[m][i]>nlstate) {
                                           dcwave[i]=m;
                                           /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                                           break;
                                   }
       }
                   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
                                   ageexmed[i]=agev[mw[1][i]][i];
                                   j=wav[i];
                                   agecens[i]=1.; 
                                   
                                   if (ageexmed[i]> 1 && wav[i] > 0){
                                           agecens[i]=agev[mw[j][i]][i];
                                           cens[i]= 1;
                                   }else if (ageexmed[i]< 1) 
                                           cens[i]= -1;
                                   if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                                           cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
                                   ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"POW-MORT_"); 
       strcat(filerespow,fileresu);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
                                   matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
                                   printf("%f ",matcov[i][j]);
                                   fprintf(ficlog,"%f ",matcov[i][j]);
         }
         printf("\n ");  fprintf(ficlog,"\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) {
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
         fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       }
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   ageminpar=50;
                   agemaxpar=100;
       if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else{
                           printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                           fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
         printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
       printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
       free_matrix(ximort,1,NDIM,1,NDIM);
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
   #ifdef GSL
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard  */
     else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximization */
         /* mlikeli uses func not funcone */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
         globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
         /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
         likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       }
       globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
                                   if (k != i) {
                                           printf("%d%d ",i,k);
                                           fprintf(ficlog,"%d%d ",i,k);
                                           fprintf(ficres,"%1d%1d ",i,k);
                                           for(j=1; j <=ncovmodel; j++){
                                                   printf("%12.7f ",p[jk]);
                                                   fprintf(ficlog,"%12.7f ",p[jk]);
                                                   fprintf(ficres,"%12.7f ",p[jk]);
                                                   jk++; 
                                           }
                                           printf("\n");
                                           fprintf(ficlog,"\n");
                                           fprintf(ficres,"\n");
                                   }
         }
       }
       if(mle != 0){
         /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, hess, p, npar, delti, ftolhess, func);
         printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
         fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
         for(i=1,jk=1; i <=nlstate; i++){
                                   for(k=1; k <=(nlstate+ndeath); k++){
                                           if (k != i) {
                                                   printf("%d%d ",i,k);
                                                   fprintf(ficlog,"%d%d ",i,k);
                                                   for(j=1; j <=ncovmodel; j++){
                                                           printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                                                           fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                                                           jk++; 
                                                   }
                                                   printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
         }
       } /* end of hesscov and Wald tests */
                   
       /*  */
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
                                   if (j!=i) {
                                           fprintf(ficres,"%1d%1d",i,j);
                                           printf("%1d%1d",i,j);
                                           fprintf(ficlog,"%1d%1d",i,j);
                                           for(k=1; k<=ncovmodel;k++){
                                                   printf(" %.5e",delti[jk]);
                                                   fprintf(ficlog," %.5e",delti[jk]);
                                                   fprintf(ficres," %.5e",delti[jk]);
                                                   jk++;
                                           }
                                           printf("\n");
                                           fprintf(ficlog,"\n");
                                           fprintf(ficres,"\n");
                                   }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle >= 1) /* To big for the screen */
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
                                   for(j=1; j <=nlstate+ndeath; j++){
                                           if(j==i) continue;
                                           for(k=1; k<=ncovmodel;k++){
                                                   jj++;
                                                   ca[0]= k+'a'-1;ca[1]='\0';
                                                   if(itimes==1){
                                                           if(mle>=1)
                                                                   printf("#%1d%1d%d",i,j,k);
                                                           fprintf(ficlog,"#%1d%1d%d",i,j,k);
                                                           fprintf(ficres,"#%1d%1d%d",i,j,k);
                                                   }else{
                                                           if(mle>=1)
                                                                   printf("%1d%1d%d",i,j,k);
                                                           fprintf(ficlog,"%1d%1d%d",i,j,k);
                                                           fprintf(ficres,"%1d%1d%d",i,j,k);
                                                   }
                                                   ll=0;
                                                   for(li=1;li <=nlstate; li++){
                                                           for(lj=1;lj <=nlstate+ndeath; lj++){
                                                                   if(lj==li) continue;
                                                                   for(lk=1;lk<=ncovmodel;lk++){
                                                                           ll++;
                                                                           if(ll<=jj){
                                                                                   cb[0]= lk +'a'-1;cb[1]='\0';
                                                                                   if(ll<jj){
                                                                                           if(itimes==1){
                                                                                                   if(mle>=1)
                                                                                                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                                                                                                   fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                                                                                                   fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                                                                                           }else{
                                                                                                   if(mle>=1)
                                                                                                           printf(" %.5e",matcov[jj][ll]); 
                                                                                                   fprintf(ficlog," %.5e",matcov[jj][ll]); 
                                                                                                   fprintf(ficres," %.5e",matcov[jj][ll]); 
                                                                                           }
                                                                                   }else{
                                                                                           if(itimes==1){
                                                                                                   if(mle>=1)
                                                                                                           printf(" Var(%s%1d%1d)",ca,i,j);
                                                                                                   fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                                                                                                   fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                                                                                           }else{
                                                                                                   if(mle>=1)
                                                                                                           printf(" %.7e",matcov[jj][ll]); 
                                                                                                   fprintf(ficlog," %.7e",matcov[jj][ll]); 
                                                                                                   fprintf(ficres," %.7e",matcov[jj][ll]); 
                                                                                           }
                                                                                   }
                                                                           }
                                                                   } /* end lk */
                                                           } /* end lj */
                                                   } /* end li */
                                                   if(mle>=1)
                                                           printf("\n");
                                                   fprintf(ficlog,"\n");
                                                   fprintf(ficres,"\n");
                                                   numlinepar++;
                                           } /* end k*/
                                   } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
                   while(fgets(line, MAXLINE, ficpar)) {
                           /* If line starts with a # it is a comment */
                           if (line[0] == '#') {
                                   numlinepar++;
                                   fputs(line,stdout);
                                   fputs(line,ficparo);
                                   fputs(line,ficlog);
                                   continue;
                           }else
                                   break;
                   }
                   
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
       
       estepm=0;
       if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
                           
                           if (num_filled != 6) {
                                   printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                                   fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                                   goto end;
                           }
                           printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
                   }
                   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
                   /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
                   
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
       fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
                   /* 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, nqveff);
       }
       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, nqveff); */
         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,nqveff); k++){
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=nqveff;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,nqveff); k++){
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=nqveff;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<=nqveff;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<=nqveff;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,nqveff); k++){
           fprintf(ficresvpl,"\n#****** ");
                           for(j=1;j<=nqveff;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_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
       free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
       free_matrix(coqvar,1,maxwav,1,n);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       free_matrix(hess,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
       free_ivector(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);
     }
   }

Removed from v.1.125  
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  Added in v.1.224


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