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Diff for /imach/src/imach.c between versions 1.125 and 1.215

-version 1.125, 2006/04/04 15:20:31
+version 1.215, 2015/12/16 08:52:24
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.215  2015/12/16 08:52:24  brouard
+   Summary: 0.98r4 working
+   Revision 1.214  2015/12/16 06:57:54  brouard
+   Summary: temporary not working
+   Revision 1.213  2015/12/11 18:22:17  brouard
+   Summary: 0.98r4
+   Revision 1.212  2015/11/21 12:47:24  brouard
+   Summary: minor typo
+   Revision 1.211  2015/11/21 12:41:11  brouard
+   Summary: 0.98r3 with some graph of projected cross-sectional
+   Author: Nicolas Brouard
+   Revision 1.210  2015/11/18 17:41:20  brouard
+   Summary: Start working on projected prevalences
+   Revision 1.209  2015/11/17 22:12:03  brouard
+   Summary: Adding ftolpl parameter
+   Author: N Brouard
+   We had difficulties to get smoothed confidence intervals. It was due
+   to the period prevalence which wasn't computed accurately. The inner
+   parameter ftolpl is now an outer parameter of the .imach parameter
+   file after estepm. If ftolpl is small 1.e-4 and estepm too,
+   computation are long.
+   Revision 1.208  2015/11/17 14:31:57  brouard
+   Summary: temporary
+   Revision 1.207  2015/10/27 17:36:57  brouard
+   *** empty log message ***
+   Revision 1.206  2015/10/24 07:14:11  brouard
+   *** empty log message ***
+   Revision 1.205  2015/10/23 15:50:53  brouard
+   Summary: 0.98r3 some clarification for graphs on likelihood contributions
+   Revision 1.204  2015/10/01 16:20:26  brouard
+   Summary: Some new graphs of contribution to likelihood
+   Revision 1.203  2015/09/30 17:45:14  brouard
+   Summary: looking at better estimation of the hessian
+   Also a better criteria for convergence to the period prevalence And
+   therefore adding the number of years needed to converge. (The
+   prevalence in any alive state shold sum to one
+   Revision 1.202  2015/09/22 19:45:16  brouard
+   Summary: Adding some overall graph on contribution to likelihood. Might change
+   Revision 1.201  2015/09/15 17:34:58  brouard
+   Summary: 0.98r0
+   - Some new graphs like suvival functions
+   - Some bugs fixed like model=1+age+V2.
+   Revision 1.200  2015/09/09 16:53:55  brouard
+   Summary: Big bug thanks to Flavia
+   Even model=1+age+V2. did not work anymore
+   Revision 1.199  2015/09/07 14:09:23  brouard
+   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+   Revision 1.198  2015/09/03 07:14:39  brouard
+   Summary: 0.98q5 Flavia
+   Revision 1.197  2015/09/01 18:24:39  brouard
+   *** empty log message ***
+   Revision 1.196  2015/08/18 23:17:52  brouard
+   Summary: 0.98q5
+   Revision 1.195  2015/08/18 16:28:39  brouard
+   Summary: Adding a hack for testing purpose
+   After reading the title, ftol and model lines, if the comment line has
+   a q, starting with #q, the answer at the end of the run is quit. It
+   permits to run test files in batch with ctest. The former workaround was
+   $ echo q | imach foo.imach
+   Revision 1.194  2015/08/18 13:32:00  brouard
+   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+   Revision 1.193  2015/08/04 07:17:42  brouard
+   Summary: 0.98q4
+   Revision 1.192  2015/07/16 16:49:02  brouard
+   Summary: Fixing some outputs
+   Revision 1.191  2015/07/14 10:00:33  brouard
+   Summary: Some fixes
+   Revision 1.190  2015/05/05 08:51:13  brouard
+   Summary: Adding digits in output parameters (7 digits instead of 6)
+   Fix 1+age+.
+   Revision 1.189  2015/04/30 14:45:16  brouard
+   Summary: 0.98q2
+   Revision 1.188  2015/04/30 08:27:53  brouard
+   *** empty log message ***
+   Revision 1.187  2015/04/29 09:11:15  brouard
+   *** empty log message ***
+   Revision 1.186  2015/04/23 12:01:52  brouard
+   Summary: V1*age is working now, version 0.98q1
+   Some codes had been disabled in order to simplify and Vn*age was
+   working in the optimization phase, ie, giving correct MLE parameters,
+   but, as usual, outputs were not correct and program core dumped.
+   Revision 1.185  2015/03/11 13:26:42  brouard
+   Summary: Inclusion of compile and links command line for Intel Compiler
+   Revision 1.184  2015/03/11 11:52:39  brouard
+   Summary: Back from Windows 8. Intel Compiler
+   Revision 1.183  2015/03/10 20:34:32  brouard
+   Summary: 0.98q0, trying with directest, mnbrak fixed
+   We use directest instead of original Powell test; probably no
+   incidence on the results, but better justifications;
+   We fixed Numerical Recipes mnbrak routine which was wrong and gave
+   wrong results.
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
+   Revision 1.168  2014/12/22 15:17:42  brouard
+   Summary: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
    Revision 1.125  2006/04/04 15:20:31  lievre
    Errors in calculation of health expectancies. Age was not initialized.
    Forecasting file added.
    Revision 1.124  2006/03/22 17:13:53  lievre
    Parameters are printed with %lf instead of %f (more numbers after the comma).
    The log-likelihood is printed in the log file
    Revision 1.123  2006/03/20 10:52:43  brouard
    * imach.c (Module): <title> changed, corresponds to .htm file
    name. <head> headers where missing.
    * imach.c (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.122  2006/03/20 09:45:41  brouard
    (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.121  2006/03/16 17:45:01  lievre
    * imach.c (Module): Comments concerning covariates added
    * imach.c (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.120  2006/03/16 15:10:38  lievre
    (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.119  2006/03/15 17:42:26  brouard
    (Module): Bug if status = -2, the loglikelihood was
    computed as likelihood omitting the logarithm. Version O.98e
    Revision 1.118  2006/03/14 18:20:07  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.117  2006/03/14 17:16:22  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.116  2006/03/06 10:29:27  brouard
    (Module): Variance-covariance wrong links and
    varian-covariance of ej. is needed (Saito).
    Revision 1.115  2006/02/27 12:17:45  brouard
    (Module): One freematrix added in mlikeli! 0.98c
    Revision 1.114  2006/02/26 12:57:58  brouard
    (Module): Some improvements in processing parameter
    filename with strsep.
    Revision 1.113  2006/02/24 14:20:24  brouard
    (Module): Memory leaks checks with valgrind and:
    datafile was not closed, some imatrix were not freed and on matrix
    allocation too.
    Revision 1.112  2006/01/30 09:55:26  brouard
    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    Revision 1.111  2006/01/25 20:38:18  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    (Module): Comments can be added in data file. Missing date values
    can be a simple dot '.'.
    Revision 1.110  2006/01/25 00:51:50  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    Revision 1.109  2006/01/24 19:37:15  brouard
    (Module): Comments (lines starting with a #) are allowed in data.
    Revision 1.108  2006/01/19 18:05:42  lievre
    Gnuplot problem appeared...
    To be fixed
    Revision 1.107  2006/01/19 16:20:37  brouard
    Test existence of gnuplot in imach path
    Revision 1.106  2006/01/19 13:24:36  brouard
    Some cleaning and links added in html output
    Revision 1.105  2006/01/05 20:23:19  lievre
    *** empty log message ***
    Revision 1.104  2005/09/30 16:11:43  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    (Module): If the status is missing at the last wave but we know
    that the person is alive, then we can code his/her status as -2
    (instead of missing=-1 in earlier versions) and his/her
    contributions to the likelihood is 1 - Prob of dying from last
    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    the healthy state at last known wave). Version is 0.98
    Revision 1.103  2005/09/30 15:54:49  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    Revision 1.102  2004/09/15 17:31:30  brouard
    Add the possibility to read data file including tab characters.
    Revision 1.101  2004/09/15 10:38:38  brouard
    Fix on curr_time
    Revision 1.100  2004/07/12 18:29:06  brouard
    Add version for Mac OS X. Just define UNIX in Makefile
    Revision 1.99  2004/06/05 08:57:40  brouard
    *** empty log message ***
    Revision 1.98  2004/05/16 15:05:56  brouard
    New version 0.97 . First attempt to estimate force of mortality
    directly from the data i.e. without the need of knowing the health
    state at each age, but using a Gompertz model: log u =a + b*age .
    This is the basic analysis of mortality and should be done before any
    other analysis, in order to test if the mortality estimated from the
    cross-longitudinal survey is different from the mortality estimated
    from other sources like vital statistic data.
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
    the slope with 95% confident intervals.
    Current limitations:
    A) Even if you enter covariates, i.e. with the
    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    B) There is no computation of Life Expectancy nor Life Table.
    Revision 1.97  2004/02/20 13:25:42  lievre
    Version 0.96d. Population forecasting command line is (temporarily)
    suppressed.
    Revision 1.96  2003/07/15 15:38:55  brouard
    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs.
    Revision 1.95  2003/07/08 07:54:34  brouard
    * imach.c (Repository):
    (Repository): Using imachwizard code to output a more meaningful covariance
    matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
    Revision 1.93  2003/06/25 16:33:55  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    (Module): Version 0.96b
    Revision 1.92  2003/06/25 16:30:45  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    Revision 1.91  2003/06/25 15:30:29  brouard
    * imach.c (Repository): Duplicated warning errors corrected.
    (Repository): Elapsed time after each iteration is now output. It
    helps to forecast when convergence will be reached. Elapsed time
    is stamped in powell.  We created a new html file for the graphs
    concerning matrix of covariance. It has extension -cov.htm.
    Revision 1.90  2003/06/24 12:34:15  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.88  2003/06/23 17:54:56  brouard
    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    Revision 1.87  2003/06/18 12:26:01  brouard
    Version 0.96
    Revision 1.86  2003/06/17 20:04:08  brouard
    (Module): Change position of html and gnuplot routines and added
    routine fileappend.
    Revision 1.85  2003/06/17 13:12:43  brouard
    * imach.c (Repository): Check when date of death was earlier that
    current date of interview. It may happen when the death was just
    prior to the death. In this case, dh was negative and likelihood
    was wrong (infinity). We still send an "Error" but patch by
    assuming that the date of death was just one stepm after the
    interview.
    (Repository): Because some people have very long ID (first column)
    we changed int to long in num[] and we added a new lvector for
    memory allocation. But we also truncated to 8 characters (left
    truncation)
    (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
    Revision 1.82  2003/06/05 15:57:20  brouard
    Add log in  imach.c and  fullversion number is now printed.
  */
  /*
     Interpolated Markov Chain
    Short summary of the programme:
    This program computes Healthy Life Expectancies from
    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    first survey ("cross") where individuals from different ages are
    interviewed on their health status or degree of disability (in the
    case of a health survey which is our main interest) -2- at least a
    second wave of interviews ("longitudinal") which measure each change
    (if any) in individual health status.  Health expectancies are
    computed from the time spent in each health state according to a
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
    probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
    complex model than "constant and age", you should modify the program
    where the markup *Covariates have to be included here again* invites
    you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
    multinomial logistic model, is clear when the delay between waves is not
    identical for each individual. Also, if a individual missed an
    intermediate interview, the information is lost, but taken into
    account using an interpolation or extrapolation.
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
    states. This elementary transition (by month, quarter,
    semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
  /*
    main
    read parameterfile
    read datafile
    concatwav
    freqsummary
    if (mle >= 1)
      mlikeli
    print results files
    if mle==1
       computes hessian
    read end of parameter file: agemin, agemax, bage, fage, estepm
        begin-prev-date,...
    open gnuplot file
    open html file
-   period (stable) prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
-   forecasting if prevfcast==1 prevforecast call prevalence()
-   health expectancies
+   h Pij x                         | pij_nom  ficrestpij
-   Variance-covariance of DFLE
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
-   prevalence()
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
-    movingaverage()
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
-   varevsij()
-   if popbased==1 varevsij(,popbased)
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
-   total life expectancies
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
-   Variance of period (stable) prevalence
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
-  end
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- */
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
- #include <math.h>
+   prevalence()
- #include <stdio.h>
+    movingaverage()
- #include <stdlib.h>
+   varevsij()
- #include <string.h>
+   if popbased==1 varevsij(,popbased)
- #include <unistd.h>
+   total life expectancies
+   Variance of period (stable) prevalence
- #include <limits.h>
+  end
- #include <sys/types.h>
+ */
- #include <sys/stat.h>
- #include <errno.h>
+ /* #define DEBUG */
- extern int errno;
+ /* #define DEBUGBRENT */
+ /* #define DEBUGLINMIN */
- /* #include <sys/time.h> */
+ /* #define DEBUGHESS */
- #include <time.h>
+ #define DEBUGHESSIJ
- #include "timeval.h"
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
+ #define POWELL /* Instead of NLOPT */
- /* #include <libintl.h> */
+ #define POWELLF1F3 /* Skip test */
- /* #define _(String) gettext (String) */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
- #define MAXLINE 256
+ #include <math.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <stdio.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <stdlib.h>
- #define FILENAMELENGTH 132
+ #include <string.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #ifdef _WIN32
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <io.h>
+ #include <windows.h>
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #include <tchar.h>
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #else
+ #include <unistd.h>
- #define NINTERVMAX 8
+ #endif
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #include <limits.h>
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #include <sys/types.h>
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #if defined(__GNUC__)
- #define AGESUP 130
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- #define AGEBASE 40
+ #endif
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #ifdef UNIX
+ #include <sys/stat.h>
- #define DIRSEPARATOR '/'
+ #include <errno.h>
- #define CHARSEPARATOR "/"
+ /* extern int errno; */
- #define ODIRSEPARATOR '\\'
- #else
+ /* #ifdef LINUX */
- #define DIRSEPARATOR '\\'
+ /* #include <time.h> */
- #define CHARSEPARATOR "\\"
+ /* #include "timeval.h" */
- #define ODIRSEPARATOR '/'
+ /* #else */
- #endif
+ /* #include <sys/time.h> */
+ /* #endif */
- /* $Id$ */
- /* $State$ */
+ #include <time.h>
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #ifdef GSL
- char fullversion[]="$Revision$ $Date$";
+ #include <gsl/gsl_errno.h>
- char strstart[80];
+ #include <gsl/gsl_multimin.h>
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #endif
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #ifdef NLOPT
- int npar=NPARMAX;
+ #include <nlopt.h>
- int nlstate=2; /* Number of live states */
+ typedef struct {
- int ndeath=1; /* Number of dead states */
+   double (* function)(double [] );
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ } myfunc_data ;
- int popbased=0;
+ #endif
- int *wav; /* Number of waves for this individuual 0 is possible */
+ /* #include <libintl.h> */
- int maxwav; /* Maxim number of waves */
+ /* #define _(String) gettext (String) */
- int jmin, jmax; /* min, max spacing between 2 waves */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define GNUPLOTPROGRAM "gnuplot"
- int mle, weightopt;
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define FILENAMELENGTH 132
- 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
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- double jmean; /* Mean space between 2 waves */
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficlog, *ficrespow;
+ #define NINTERVMAX 8
- int globpr; /* Global variable for printing or not */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- double fretone; /* Only one call to likelihood */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- long ipmx; /* Number of contributions */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- double sw; /* Sum of weights */
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
- char filerespow[FILENAMELENGTH];
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- FILE *ficresilk;
+ #define MAXN 20000
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define YEARM 12. /**< Number of months per year */
- FILE *ficresprobmorprev;
+ #define AGESUP 130
- FILE *fichtm, *fichtmcov; /* Html File */
+ #define AGEBASE 40
- FILE *ficreseij;
+ #define AGEOVERFLOW 1.e20
- char filerese[FILENAMELENGTH];
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- FILE *ficresstdeij;
+ #ifdef _WIN32
- char fileresstde[FILENAMELENGTH];
+ #define DIRSEPARATOR '\\'
- FILE *ficrescveij;
+ #define CHARSEPARATOR "\\"
- char filerescve[FILENAMELENGTH];
+ #define ODIRSEPARATOR '/'
- FILE  *ficresvij;
+ #else
- char fileresv[FILENAMELENGTH];
+ #define DIRSEPARATOR '/'
- FILE  *ficresvpl;
+ #define CHARSEPARATOR "/"
- char fileresvpl[FILENAMELENGTH];
+ #define ODIRSEPARATOR '\\'
- char title[MAXLINE];
+ #endif
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ /* $Id$ */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ /* $State$ */
- char command[FILENAMELENGTH];
+ #include "version.h"
- int  outcmd=0;
+ char version[]=__IMACH_VERSION__;
+ char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
- char filelog[FILENAMELENGTH]; /* Log file */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- char filerest[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char fileregp[FILENAMELENGTH];
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- char popfile[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ 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 */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- struct timezone tzp;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- extern int gettimeofday();
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int cptcov=0; /* Working variable */
- long time_value;
+ int npar=NPARMAX;
- extern long time();
+ int nlstate=2; /* Number of live states */
- char strcurr[80], strfor[80];
+ int ndeath=1; /* Number of dead states */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char *endptr;
+ int popbased=0;
- long lval;
- double dval;
+ int *wav; /* Number of waves for this individuual 0 is possible */
+ int maxwav=0; /* Maxim number of waves */
- #define NR_END 1
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- #define FREE_ARG char*
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- #define FTOL 1.0e-10
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
- #define NRANSI
+ int mle=1, weightopt=0;
- #define ITMAX 200
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- #define TOL 2.0e-4
+ 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. */
- #define CGOLD 0.3819660
+ int countcallfunc=0;  /* Count the number of calls to func */
- #define ZEPS 1.0e-10
+ double jmean=1; /* Mean space between 2 waves */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ double **matprod2(); /* test */
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define GOLD 1.618034
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- #define GLIMIT 100.0
+ /*FILE *fic ; */ /* Used in readdata only */
- #define TINY 1.0e-20
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficlog, *ficrespow;
- static double maxarg1,maxarg2;
+ int globpr=0; /* Global variable for printing or not */
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ double fretone; /* Only one call to likelihood */
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char filerespow[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
- static double sqrarg;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ FILE *ficresprobmorprev;
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ FILE *fichtm, *fichtmcov; /* Html File */
- int agegomp= AGEGOMP;
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
- int imx;
+ FILE *ficresstdeij;
- int stepm=1;
+ char fileresstde[FILENAMELENGTH];
- /* Stepm, step in month: minimum step interpolation*/
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
- int estepm;
+ FILE  *ficresvij;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
- int m,nb;
+ char fileresvpl[FILENAMELENGTH];
- long *num;
+ char title[MAXLINE];
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- double **pmmij, ***probs;
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- double *ageexmed,*agecens;
+ char command[FILENAMELENGTH];
- double dateintmean=0;
+ int  outcmd=0;
- double *weight;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- int **s; /* Status */
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
- double *agedc, **covar, idx;
+ char filelog[FILENAMELENGTH]; /* Log file */
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ char filerest[FILENAMELENGTH];
- double *lsurv, *lpop, *tpop;
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- /**************** split *************************/
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ /* struct timezone tzp; */
- {
+ /* extern int gettimeofday(); */
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ struct tm tml, *gmtime(), *localtime();
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ extern time_t time();
-   char  *ss;                            /* pointer */
-   int   l1, l2;                         /* length counters */
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
-   l1 = strlen(path );                   /* length of path */
+ struct tm tm;
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ char strcurr[80], strfor[80];
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ char *endptr;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ long lval;
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ double dval;
-     /* get current working directory */
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define NR_END 1
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define FREE_ARG char*
-       return( GLOCK_ERROR_GETCWD );
+ #define FTOL 1.0e-10
-     }
-     /* got dirc from getcwd*/
+ #define NRANSI
-     printf(" DIRC = %s \n",dirc);
+ #define ITMAX 200
-   } else {                              /* strip direcotry from path */
-     ss++;                               /* after this, the filename */
+ #define TOL 2.0e-4
-     l2 = strlen( ss );                  /* length of filename */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define CGOLD 0.3819660
-     strcpy( name, ss );         /* save file name */
+ #define ZEPS 1.0e-10
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     dirc[l1-l2] = 0;                    /* add zero */
-     printf(" DIRC2 = %s \n",dirc);
+ #define GOLD 1.618034
-   }
+ #define GLIMIT 100.0
-   /* We add a separator at the end of dirc if not exists */
+ #define TINY 1.0e-20
-   l1 = strlen( dirc );                  /* length of directory */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ static double maxarg1,maxarg2;
-     dirc[l1] =  DIRSEPARATOR;
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     dirc[l1+1] = 0;
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     printf(" DIRC3 = %s \n",dirc);
-   }
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   ss = strrchr( name, '.' );            /* find last / */
+ #define rint(a) floor(a+0.5)
-   if (ss >0){
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     ss++;
+ #define mytinydouble 1.0e-16
-     strcpy(ext,ss);                     /* save extension */
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     l1= strlen( name);
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-     l2= strlen(ss)+1;
+ /* static double dsqrarg; */
-     strncpy( finame, name, l1-l2);
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-     finame[l1-l2]= 0;
+ static double sqrarg;
-   }
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   return( 0 );                          /* we're done */
+ int agegomp= AGEGOMP;
- }
+ int imx;
+ int stepm=1;
- /******************************************/
+ /* Stepm, step in month: minimum step interpolation*/
- void replace_back_to_slash(char *s, char*t)
+ int estepm;
- {
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-   int i;
-   int lg=0;
+ int m,nb;
-   i=0;
+ long *num;
-   lg=strlen(t);
+ int firstpass=0, lastpass=4,*cod, *cens;
-   for(i=0; i<= lg; i++) {
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
-     (s[i] = t[i]);
+                    covariate for which somebody answered excluding
-     if (t[i]== '\\') s[i]='/';
+                    undefined. Usually 2: 0 and 1. */
-   }
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
- }
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
- int nbocc(char *s, char occ)
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- {
+ double **pmmij, ***probs;
-   int i,j=0;
+ double *ageexmed,*agecens;
-   int lg=20;
+ double dateintmean=0;
-   i=0;
-   lg=strlen(s);
+ double *weight;
-   for(i=0; i<= lg; i++) {
+ int **s; /* Status */
-   if  (s[i] == occ ) j++;
+ double *agedc;
-   }
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   return j;
+                   * covar=matrix(0,NCOVMAX,1,n);
- }
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
+ double  idx;
- void cutv(char *u,char *v, char*t, char occ)
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- {
+ int *Tage;
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ int *Ndum; /** Freq of modality (tricode */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
-      gives u="abcedf" and v="ghi2j" */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   int i,lg,j,p=0;
+ double *lsurv, *lpop, *tpop;
-   i=0;
-   for(j=0; j<=strlen(t)-1; j++) {
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ double ftolhess; /**< Tolerance for computing hessian */
-   }
+ /**************** split *************************/
-   lg=strlen(t);
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   for(j=0; j<p; j++) {
+ {
-     (u[j] = t[j]);
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   }
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-      u[p]='\0';
+   */
+   char  *ss;                            /* pointer */
-    for(j=0; j<= lg; j++) {
+   int   l1=0, l2=0;                             /* length counters */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
-   }
+   l1 = strlen(path );                   /* length of path */
- }
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- /********************** nrerror ********************/
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
- void nrerror(char error_text[])
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
- {
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   fprintf(stderr,"ERREUR ...\n");
+     /* get current working directory */
-   fprintf(stderr,"%s\n",error_text);
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   exit(EXIT_FAILURE);
+ #ifdef WIN32
- }
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
- /*********************** vector *******************/
+ #else
- double *vector(int nl, int nh)
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
- {
+ #endif
-   double *v;
+       return( GLOCK_ERROR_GETCWD );
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     }
-   if (!v) nrerror("allocation failure in vector");
+     /* got dirc from getcwd*/
-   return v-nl+NR_END;
+     printf(" DIRC = %s \n",dirc);
- }
+   } else {                              /* strip directory from path */
+     ss++;                               /* after this, the filename */
- /************************ free vector ******************/
+     l2 = strlen( ss );                  /* length of filename */
- void free_vector(double*v, int nl, int nh)
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
- {
+     strcpy( name, ss );         /* save file name */
-   free((FREE_ARG)(v+nl-NR_END));
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
- }
+     dirc[l1-l2] = '\0';                 /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
- /************************ivector *******************************/
+   }
- int *ivector(long nl,long nh)
+   /* We add a separator at the end of dirc if not exists */
- {
+   l1 = strlen( dirc );                  /* length of directory */
-   int *v;
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+     dirc[l1] =  DIRSEPARATOR;
-   if (!v) nrerror("allocation failure in ivector");
+     dirc[l1+1] = 0;
-   return v-nl+NR_END;
+     printf(" DIRC3 = %s \n",dirc);
- }
+   }
+   ss = strrchr( name, '.' );            /* find last / */
- /******************free ivector **************************/
+   if (ss >0){
- void free_ivector(int *v, long nl, long nh)
+     ss++;
- {
+     strcpy(ext,ss);                     /* save extension */
-   free((FREE_ARG)(v+nl-NR_END));
+     l1= strlen( name);
- }
+     l2= strlen(ss)+1;
+     strncpy( finame, name, l1-l2);
- /************************lvector *******************************/
+     finame[l1-l2]= 0;
- long *lvector(long nl,long nh)
+   }
- {
-   long *v;
+   return( 0 );                          /* we're done */
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ }
-   if (!v) nrerror("allocation failure in ivector");
-   return v-nl+NR_END;
- }
+ /******************************************/
- /******************free lvector **************************/
+ void replace_back_to_slash(char *s, char*t)
- void free_lvector(long *v, long nl, long nh)
+ {
- {
+   int i;
-   free((FREE_ARG)(v+nl-NR_END));
+   int lg=0;
- }
+   i=0;
+   lg=strlen(t);
- /******************* imatrix *******************************/
+   for(i=0; i<= lg; i++) {
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+     (s[i] = t[i]);
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+     if (t[i]== '\\') s[i]='/';
- {
+   }
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ }
-   int **m;
+ char *trimbb(char *out, char *in)
-   /* allocate pointers to rows */
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   char *s;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   s=out;
-   m += NR_END;
+   while (*in != '\0'){
-   m -= nrl;
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
+     }
-   /* allocate rows and set pointers to them */
+     *out++ = *in++;
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   *out='\0';
-   m[nrl] += NR_END;
+   return s;
-   m[nrl] -= ncl;
+ }
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ /* char *substrchaine(char *out, char *in, char *chain) */
+ /* { */
-   /* return pointer to array of pointers to rows */
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
-   return m;
+ /*   char *s, *t; */
- }
+ /*   t=in;s=out; */
+ /*   while ((*in != *chain) && (*in != '\0')){ */
- /****************** free_imatrix *************************/
+ /*     *out++ = *in++; */
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ /*   } */
-       int **m;
-       long nch,ncl,nrh,nrl;
+ /*   /\* *in matches *chain *\/ */
-      /* free an int matrix allocated by imatrix() */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
- {
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ /*   } */
-   free((FREE_ARG) (m+nrl-NR_END));
+ /*   in--; chain--; */
- }
+ /*   while ( (*in != '\0')){ */
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- /******************* matrix *******************************/
+ /*     *out++ = *in++; */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- {
+ /*   } */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ /*   *out='\0'; */
-   double **m;
+ /*   out=s; */
+ /*   return out; */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /* } */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ char *substrchaine(char *out, char *in, char *chain)
-   m += NR_END;
+ {
-   m -= nrl;
+   /* Substract chain 'chain' from 'in', return and output 'out' */
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   char *strloc;
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+   strcpy (out, in);
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
-   return m;
+   if(strloc != NULL){
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
-    */
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
- }
+     /* strcpy (strloc, strloc +strlen(chain));*/
+   }
- /*************************free matrix ************************/
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   return out;
- {
+ }
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
+ {
- /******************* ma3x *******************************/
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- {
+      gives blocc="abcdef" and alocc="ghi2j".
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-   double ***m;
+   */
+   char *s, *t;
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   t=in;s=in;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   while ((*in != occ) && (*in != '\0')){
-   m += NR_END;
+     *alocc++ = *in++;
-   m -= nrl;
+   }
+   if( *in == occ){
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     *(alocc)='\0';
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     s=++in;
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   if (s == t) {/* occ not found */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+     *(alocc-(in-s))='\0';
+     in=s;
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+   }
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   while ( *in != '\0'){
-   m[nrl][ncl] += NR_END;
+     *blocc++ = *in++;
-   m[nrl][ncl] -= nll;
+   }
-   for (j=ncl+1; j<=nch; j++)
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   *blocc='\0';
+   return t;
-   for (i=nrl+1; i<=nrh; i++) {
+ }
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-     for (j=ncl+1; j<=nch; j++)
+ {
-       m[i][j]=m[i][j-1]+nlay;
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
-   }
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   return m;
+      gives blocc="abcdef2ghi" and alocc="j".
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   */
-   */
+   char *s, *t;
- }
+   t=in;s=in;
+   while (*in != '\0'){
- /*************************free ma3x ************************/
+     while( *in == occ){
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+       *blocc++ = *in++;
- {
+       s=in;
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+     }
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+     *blocc++ = *in++;
-   free((FREE_ARG)(m+nrl-NR_END));
+   }
- }
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
- /*************** function subdirf ***********/
+   else
- char *subdirf(char fileres[])
+     *(blocc-(in-s)-1)='\0';
- {
+   in=s;
-   /* Caution optionfilefiname is hidden */
+   while ( *in != '\0'){
-   strcpy(tmpout,optionfilefiname);
+     *alocc++ = *in++;
-   strcat(tmpout,"/"); /* Add to the right */
+   }
-   strcat(tmpout,fileres);
-   return tmpout;
+   *alocc='\0';
- }
+   return s;
+ }
- /*************** function subdirf2 ***********/
- char *subdirf2(char fileres[], char *preop)
+ int nbocc(char *s, char occ)
  {
+   int i,j=0;
-   /* Caution optionfilefiname is hidden */
+   int lg=20;
-   strcpy(tmpout,optionfilefiname);
+   i=0;
-   strcat(tmpout,"/");
+   lg=strlen(s);
-   strcat(tmpout,preop);
+   for(i=0; i<= lg; i++) {
-   strcat(tmpout,fileres);
+   if  (s[i] == occ ) j++;
-   return tmpout;
+   }
- }
+   return j;
+ }
- /*************** function subdirf3 ***********/
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   /* Caution optionfilefiname is hidden */
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   strcpy(tmpout,optionfilefiname);
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   strcat(tmpout,"/");
+ /*   int i,lg,j,p=0; */
-   strcat(tmpout,preop);
+ /*   i=0; */
-   strcat(tmpout,preop2);
+ /*   lg=strlen(t); */
-   strcat(tmpout,fileres);
+ /*   for(j=0; j<=lg-1; j++) { */
-   return tmpout;
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
- }
+ /*   } */
- /***************** f1dim *************************/
+ /*   for(j=0; j<p; j++) { */
- extern int ncom;
+ /*     (u[j] = t[j]); */
- extern double *pcom,*xicom;
+ /*   } */
- extern double (*nrfunc)(double []);
+ /*      u[p]='\0'; */
- double f1dim(double x)
+ /*    for(j=0; j<= lg; j++) { */
- {
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   int j;
+ /*   } */
-   double f;
+ /* } */
-   double *xt;
+ #ifdef _WIN32
-   xt=vector(1,ncom);
+ char * strsep(char **pp, const char *delim)
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ {
-   f=(*nrfunc)(xt);
+   char *p, *q;
-   free_vector(xt,1,ncom);
-   return f;
+   if ((p = *pp) == NULL)
- }
+     return 0;
+   if ((q = strpbrk (p, delim)) != NULL)
- /*****************brent *************************/
+   {
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+     *pp = q + 1;
- {
+     *q = '\0';
-   int iter;
+   }
-   double a,b,d,etemp;
+   else
-   double fu,fv,fw,fx;
+     *pp = 0;
-   double ftemp;
+   return p;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ }
-   double e=0.0;
+ #endif
-   a=(ax < cx ? ax : cx);
+ /********************** nrerror ********************/
-   b=(ax > cx ? ax : cx);
-   x=w=v=bx;
+ void nrerror(char error_text[])
-   fw=fv=fx=(*f)(x);
+ {
-   for (iter=1;iter<=ITMAX;iter++) {
+   fprintf(stderr,"ERREUR ...\n");
-     xm=0.5*(a+b);
+   fprintf(stderr,"%s\n",error_text);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   exit(EXIT_FAILURE);
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ }
-     printf(".");fflush(stdout);
+ /*********************** vector *******************/
-     fprintf(ficlog,".");fflush(ficlog);
+ double *vector(int nl, int nh)
- #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);
+   double *v;
-     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);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   if (!v) nrerror("allocation failure in vector");
- #endif
+   return v-nl+NR_END;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ }
-       *xmin=x;
-       return fx;
+ /************************ free vector ******************/
-     }
+ void free_vector(double*v, int nl, int nh)
-     ftemp=fu;
+ {
-     if (fabs(e) > tol1) {
+   free((FREE_ARG)(v+nl-NR_END));
-       r=(x-w)*(fx-fv);
+ }
-       q=(x-v)*(fx-fw);
-       p=(x-v)*q-(x-w)*r;
+ /************************ivector *******************************/
-       q=2.0*(q-r);
+ int *ivector(long nl,long nh)
-       if (q > 0.0) p = -p;
+ {
-       q=fabs(q);
+   int *v;
-       etemp=e;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-       e=d;
+   if (!v) nrerror("allocation failure in ivector");
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   return v-nl+NR_END;
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ }
-       else {
-         d=p/q;
+ /******************free ivector **************************/
-         u=x+d;
+ void free_ivector(int *v, long nl, long nh)
-         if (u-a < tol2 || b-u < tol2)
+ {
-           d=SIGN(tol1,xm-x);
+   free((FREE_ARG)(v+nl-NR_END));
-       }
+ }
-     } else {
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /************************lvector *******************************/
-     }
+ long *lvector(long nl,long nh)
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ {
-     fu=(*f)(u);
+   long *v;
-     if (fu <= fx) {
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-       if (u >= x) a=x; else b=x;
+   if (!v) nrerror("allocation failure in ivector");
-       SHFT(v,w,x,u)
+   return v-nl+NR_END;
-         SHFT(fv,fw,fx,fu)
+ }
-         } else {
-           if (u < x) a=u; else b=u;
+ /******************free lvector **************************/
-           if (fu <= fw || w == x) {
+ void free_lvector(long *v, long nl, long nh)
-             v=w;
+ {
-             w=u;
+   free((FREE_ARG)(v+nl-NR_END));
-             fv=fw;
+ }
-             fw=fu;
-           } else if (fu <= fv || v == x || v == w) {
+ /******************* imatrix *******************************/
-             v=u;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-             fv=fu;
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-           }
+ {
-         }
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   }
+   int **m;
-   nrerror("Too many iterations in brent");
-   *xmin=x;
+   /* allocate pointers to rows */
-   return fx;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- }
+   if (!m) nrerror("allocation failure 1 in matrix()");
+   m += NR_END;
- /****************** mnbrak ***********************/
+   m -= nrl;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-             double (*func)(double))
+   /* allocate rows and set pointers to them */
- {
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   double ulim,u,r,q, dum;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   double fu;
+   m[nrl] += NR_END;
+   m[nrl] -= ncl;
-   *fa=(*func)(*ax);
-   *fb=(*func)(*bx);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   if (*fb > *fa) {
-     SHFT(dum,*ax,*bx,dum)
+   /* return pointer to array of pointers to rows */
-       SHFT(dum,*fb,*fa,dum)
+   return m;
-       }
+ }
-   *cx=(*bx)+GOLD*(*bx-*ax);
-   *fc=(*func)(*cx);
+ /****************** free_imatrix *************************/
-   while (*fb > *fc) {
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-     r=(*bx-*ax)*(*fb-*fc);
+       int **m;
-     q=(*bx-*cx)*(*fb-*fa);
+       long nch,ncl,nrh,nrl;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+      /* free an int matrix allocated by imatrix() */
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+ {
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   free((FREE_ARG) (m+nrl-NR_END));
-       fu=(*func)(u);
+ }
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       fu=(*func)(u);
+ /******************* matrix *******************************/
-       if (fu < *fc) {
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ {
-           SHFT(*fb,*fc,fu,(*func)(u))
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-           }
+   double **m;
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-       u=ulim;
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       fu=(*func)(u);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     } else {
+   m += NR_END;
-       u=(*cx)+GOLD*(*cx-*bx);
+   m -= nrl;
-       fu=(*func)(u);
-     }
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-     SHFT(*ax,*bx,*cx,u)
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       SHFT(*fa,*fb,*fc,fu)
+   m[nrl] += NR_END;
-       }
+   m[nrl] -= ncl;
- }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- /*************** linmin ************************/
+   return m;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
- int ncom;
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
- double *pcom,*xicom;
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
- double (*nrfunc)(double []);
+    */
+ }
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
- {
+ /*************************free matrix ************************/
-   double brent(double ax, double bx, double cx,
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-                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;
+ /******************* ma3x *******************************/
-   double fx,fb,fa;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ {
-   ncom=n;
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+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);
- #endif
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   for (j=1;j<=n;j++) {
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-     xi[j] *= xmin;
+   m[nrl][ncl] += NR_END;
-     p[j] += xi[j];
+   m[nrl][ncl] -= nll;
-   }
+   for (j=ncl+1; j<=nch; j++)
-   free_vector(xicom,1,n);
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   free_vector(pcom,1,n);
- }
+   for (i=nrl+1; i<=nrh; i++) {
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- char *asc_diff_time(long time_sec, char ascdiff[])
+     for (j=ncl+1; j<=nch; j++)
- {
+       m[i][j]=m[i][j-1]+nlay;
-   long sec_left, days, hours, minutes;
+   }
-   days = (time_sec) / (60*60*24);
+   return m;
-   sec_left = (time_sec) % (60*60*24);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   hours = (sec_left) / (60*60) ;
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   sec_left = (sec_left) %(60*60);
+   */
-   minutes = (sec_left) /60;
+ }
-   sec_left = (sec_left) % (60);
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ /*************************free ma3x ************************/
-   return ascdiff;
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
- }
+ {
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
- /*************** powell ************************/
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   free((FREE_ARG)(m+nrl-NR_END));
-             double (*func)(double []))
+ }
- {
-   void linmin(double p[], double xi[], int n, double *fret,
+ /*************** function subdirf ***********/
-               double (*func)(double []));
+ char *subdirf(char fileres[])
-   int i,ibig,j;
+ {
-   double del,t,*pt,*ptt,*xit;
+   /* Caution optionfilefiname is hidden */
-   double fp,fptt;
+   strcpy(tmpout,optionfilefiname);
-   double *xits;
+   strcat(tmpout,"/"); /* Add to the right */
-   int niterf, itmp;
+   strcat(tmpout,fileres);
+   return tmpout;
-   pt=vector(1,n);
+ }
-   ptt=vector(1,n);
-   xit=vector(1,n);
+ /*************** function subdirf2 ***********/
-   xits=vector(1,n);
+ char *subdirf2(char fileres[], char *preop)
-   *fret=(*func)(p);
+ {
-   for (j=1;j<=n;j++) pt[j]=p[j];
-   for (*iter=1;;++(*iter)) {
+   /* Caution optionfilefiname is hidden */
-     fp=(*fret);
+   strcpy(tmpout,optionfilefiname);
-     ibig=0;
+   strcat(tmpout,"/");
-     del=0.0;
+   strcat(tmpout,preop);
-     last_time=curr_time;
+   strcat(tmpout,fileres);
-     (void) gettimeofday(&curr_time,&tzp);
+   return tmpout;
-     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); */
+ /*************** function subdirf3 ***********/
-    for (i=1;i<=n;i++) {
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-       printf(" %d %.12f",i, p[i]);
+ {
-       fprintf(ficlog," %d %.12lf",i, p[i]);
-       fprintf(ficrespow," %.12lf", p[i]);
+   /* Caution optionfilefiname is hidden */
-     }
+   strcpy(tmpout,optionfilefiname);
-     printf("\n");
+   strcat(tmpout,"/");
-     fprintf(ficlog,"\n");
+   strcat(tmpout,preop);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   strcat(tmpout,preop2);
-     if(*iter <=3){
+   strcat(tmpout,fileres);
-       tm = *localtime(&curr_time.tv_sec);
+   return tmpout;
-       strcpy(strcurr,asctime(&tm));
+ }
- /*       asctime_r(&tm,strcurr); */
-       forecast_time=curr_time;
+ /*************** function subdirfext ***********/
-       itmp = strlen(strcurr);
+ char *subdirfext(char fileres[], char *preop, char *postop)
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+ {
-         strcurr[itmp-1]='\0';
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   strcpy(tmpout,preop);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   strcat(tmpout,fileres);
-       for(niterf=10;niterf<=30;niterf+=10){
+   strcat(tmpout,postop);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+   return tmpout;
-         tmf = *localtime(&forecast_time.tv_sec);
+ }
- /*      asctime_r(&tmf,strfor); */
-         strcpy(strfor,asctime(&tmf));
+ /*************** function subdirfext3 ***********/
-         itmp = strlen(strfor);
+ char *subdirfext3(char fileres[], char *preop, char *postop)
-         if(strfor[itmp-1]=='\n')
+ {
-         strfor[itmp-1]='\0';
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   /* Caution optionfilefiname is hidden */
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   strcpy(tmpout,optionfilefiname);
-       }
+   strcat(tmpout,"/");
-     }
+   strcat(tmpout,preop);
-     for (i=1;i<=n;i++) {
+   strcat(tmpout,fileres);
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   strcat(tmpout,postop);
-       fptt=(*fret);
+   return tmpout;
- #ifdef DEBUG
+ }
-       printf("fret=%lf \n",*fret);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+ char *asc_diff_time(long time_sec, char ascdiff[])
- #endif
+ {
-       printf("%d",i);fflush(stdout);
+   long sec_left, days, hours, minutes;
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+   days = (time_sec) / (60*60*24);
-       linmin(p,xit,n,fret,func);
+   sec_left = (time_sec) % (60*60*24);
-       if (fabs(fptt-(*fret)) > del) {
+   hours = (sec_left) / (60*60) ;
-         del=fabs(fptt-(*fret));
+   sec_left = (sec_left) %(60*60);
-         ibig=i;
+   minutes = (sec_left) /60;
-       }
+   sec_left = (sec_left) % (60);
- #ifdef DEBUG
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-       printf("%d %.12e",i,(*fret));
+   return ascdiff;
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+ }
-       for (j=1;j<=n;j++) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+ /***************** f1dim *************************/
-         printf(" x(%d)=%.12e",j,xit[j]);
+ extern int ncom;
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+ extern double *pcom,*xicom;
-       }
+ extern double (*nrfunc)(double []);
-       for(j=1;j<=n;j++) {
-         printf(" p=%.12e",p[j]);
+ double f1dim(double x)
-         fprintf(ficlog," p=%.12e",p[j]);
+ {
-       }
+   int j;
-       printf("\n");
+   double f;
-       fprintf(ficlog,"\n");
+   double *xt;
- #endif
-     }
+   xt=vector(1,ncom);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
- #ifdef DEBUG
+   f=(*nrfunc)(xt);
-       int k[2],l;
+   free_vector(xt,1,ncom);
-       k[0]=1;
+   return f;
-       k[1]=-1;
+ }
-       printf("Max: %.12e",(*func)(p));
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+ /*****************brent *************************/
-       for (j=1;j<=n;j++) {
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-         printf(" %.12e",p[j]);
+ {
-         fprintf(ficlog," %.12e",p[j]);
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       }
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-       printf("\n");
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
-       fprintf(ficlog,"\n");
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
-       for(l=0;l<=1;l++) {
+    * returned function value.
-         for (j=1;j<=n;j++) {
+   */
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+   int iter;
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   double a,b,d,etemp;
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   double fu=0,fv,fw,fx;
-         }
+   double ftemp=0.;
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   double e=0.0;
-       }
- #endif
+   a=(ax < cx ? ax : cx);
+   b=(ax > cx ? ax : cx);
+   x=w=v=bx;
-       free_vector(xit,1,n);
+   fw=fv=fx=(*f)(x);
-       free_vector(xits,1,n);
+   for (iter=1;iter<=ITMAX;iter++) {
-       free_vector(ptt,1,n);
+     xm=0.5*(a+b);
-       free_vector(pt,1,n);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-       return;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     }
+     printf(".");fflush(stdout);
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     fprintf(ficlog,".");fflush(ficlog);
-     for (j=1;j<=n;j++) {
+ #ifdef DEBUGBRENT
-       ptt[j]=2.0*p[j]-pt[j];
+     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);
-       xit[j]=p[j]-pt[j];
+     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);
-       pt[j]=p[j];
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-     }
+ #endif
-     fptt=(*func)(ptt);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-     if (fptt < fp) {
+       *xmin=x;
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+       return fx;
-       if (t < 0.0) {
+     }
-         linmin(p,xit,n,fret,func);
+     ftemp=fu;
-         for (j=1;j<=n;j++) {
+     if (fabs(e) > tol1) {
-           xi[j][ibig]=xi[j][n];
+       r=(x-w)*(fx-fv);
-           xi[j][n]=xit[j];
+       q=(x-v)*(fx-fw);
-         }
+       p=(x-v)*q-(x-w)*r;
- #ifdef DEBUG
+       q=2.0*(q-r);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+       if (q > 0.0) p = -p;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+       q=fabs(q);
-         for(j=1;j<=n;j++){
+       etemp=e;
-           printf(" %.12e",xit[j]);
+       e=d;
-           fprintf(ficlog," %.12e",xit[j]);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         }
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         printf("\n");
+       else {
-         fprintf(ficlog,"\n");
+         d=p/q;
- #endif
+         u=x+d;
-       }
+         if (u-a < tol2 || b-u < tol2)
-     }
+           d=SIGN(tol1,xm-x);
-   }
+       }
- }
+     } else {
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
- /**** Prevalence limit (stable or period prevalence)  ****************/
+     }
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+     fu=(*f)(u);
- {
+     if (fu <= fx) {
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+       if (u >= x) a=x; else b=x;
-      matrix by transitions matrix until convergence is reached */
+       SHFT(v,w,x,u)
+       SHFT(fv,fw,fx,fu)
-   int i, ii,j,k;
+     } else {
-   double min, max, maxmin, maxmax,sumnew=0.;
+       if (u < x) a=u; else b=u;
-   double **matprod2();
+       if (fu <= fw || w == x) {
-   double **out, cov[NCOVMAX], **pmij();
+         v=w;
-   double **newm;
+         w=u;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+         fv=fw;
+         fw=fu;
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+       } else if (fu <= fv || v == x || v == w) {
-     for (j=1;j<=nlstate+ndeath;j++){
+         v=u;
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         fv=fu;
-     }
+       }
+     }
-    cov[1]=1.;
+   }
+   nrerror("Too many iterations in brent");
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   *xmin=x;
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+   return fx;
-     newm=savm;
+ }
-     /* Covariates have to be included here again */
-      cov[2]=agefin;
+ /****************** mnbrak ***********************/
-       for (k=1; k<=cptcovn;k++) {
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+             double (*func)(double))
-         /*      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]]);*/
+ { /* 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
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
-       for (k=1; k<=cptcovprod;k++)
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+    */
+   double ulim,u,r,q, dum;
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   double fu;
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   double scale=10.;
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   int iterscale=0;
-     savm=oldm;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
-     oldm=newm;
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
-     maxmax=0.;
-     for(j=1;j<=nlstate;j++){
-       min=1.;
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
-       max=0.;
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
-       for(i=1; i<=nlstate; i++) {
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-         sumnew=0;
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
-         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]);
+   if (*fb > *fa) {
-         min=FMIN(min,prlim[i][j]);
+     SHFT(dum,*ax,*bx,dum)
-       }
+     SHFT(dum,*fb,*fa,dum)
-       maxmin=max-min;
+   }
-       maxmax=FMAX(maxmax,maxmin);
+   *cx=(*bx)+GOLD*(*bx-*ax);
-     }
+   *fc=(*func)(*cx);
-     if(maxmax < ftolpl){
+ #ifdef DEBUG
-       return prlim;
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-     }
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-   }
+ #endif
- }
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
+     r=(*bx-*ax)*(*fb-*fc);
- /*************** transition probabilities ***************/
+     q=(*bx-*cx)*(*fb-*fa);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
- {
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-   double s1, s2;
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-   /*double t34;*/
+       fu=(*func)(u);
-   int i,j,j1, nc, ii, jj;
+ #ifdef DEBUG
+       /* f(x)=A(x-u)**2+f(u) */
-     for(i=1; i<= nlstate; i++){
+       double A, fparabu;
-       for(j=1; j<i;j++){
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-         }
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-         ps[i][j]=s2;
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-       }
+ #endif
-       for(j=i+1; j<=nlstate+ndeath;j++){
+ #ifdef MNBRAKORIGINAL
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ #else
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*       if (fu > *fc) { */
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+ /* #ifdef DEBUG */
-         }
+ /*       printf("mnbrak4  fu > fc \n"); */
-         ps[i][j]=s2;
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
-       }
+ /* #endif */
-     }
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
-     /*ps[3][2]=1;*/
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+ /*      dum=u; /\* Shifting c and u *\/ */
-     for(i=1; i<= nlstate; i++){
+ /*      u = *cx; */
-       s1=0;
+ /*      *cx = dum; */
-       for(j=1; j<i; j++)
+ /*      dum = fu; */
-         s1+=exp(ps[i][j]);
+ /*      fu = *fc; */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ /*      *fc =dum; */
-         s1+=exp(ps[i][j]);
+ /*       } else { /\* end *\/ */
-       ps[i][i]=1./(s1+1.);
+ /* #ifdef DEBUG */
-       for(j=1; j<i; j++)
+ /*       printf("mnbrak3  fu < fc \n"); */
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ /* #endif */
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /*      dum=u; /\* Shifting c and u *\/ */
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+ /*      u = *cx; */
-     } /* end i */
+ /*      *cx = dum; */
+ /*      dum = fu; */
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ /*      fu = *fc; */
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+ /*      *fc =dum; */
-         ps[ii][jj]=0;
+ /*       } */
-         ps[ii][ii]=1;
+ #ifdef DEBUG
-       }
+       printf("mnbrak34  fu < or >= fc \n");
-     }
+       fprintf(ficlog, "mnbrak34 fu < fc\n");
+ #endif
+       dum=u; /* Shifting c and u */
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       u = *cx;
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       *cx = dum;
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       dum = fu;
- /*       } */
+       fu = *fc;
- /*       printf("\n "); */
+       *fc =dum;
- /*        } */
+ #endif
- /*        printf("\n ");printf("%lf ",cov[2]); */
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-        /*
+ #ifdef DEBUG
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       printf("mnbrak2  u after c but before ulim\n");
-       goto end;*/
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
-     return ps;
+ #endif
- }
+       fu=(*func)(u);
+       if (fu < *fc) {
- /**************** Product of 2 matrices ******************/
+ #ifdef DEBUG
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
- {
+ #endif
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+         SHFT(*fb,*fc,fu,(*func)(u))
-   /* in, b, out are matrice of pointers which should have been initialized
+       }
-      before: only the contents of out is modified. The function returns
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-      a pointer to pointers identical to out */
+ #ifdef DEBUG
-   long i, j, k;
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
-   for(i=nrl; i<= nrh; i++)
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
-     for(k=ncolol; k<=ncoloh; k++)
+ #endif
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       u=ulim;
-         out[i][k] +=in[i][j]*b[j][k];
+       fu=(*func)(u);
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
-   return out;
+ #ifdef DEBUG
- }
+       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+ #endif
- /************* Higher Matrix Product ***************/
+       u=(*cx)+GOLD*(*cx-*bx);
+       fu=(*func)(u);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+     } /* end tests */
- {
+     SHFT(*ax,*bx,*cx,u)
-   /* Computes the transition matrix starting at age 'age' over
+     SHFT(*fa,*fb,*fc,fu)
-      'nhstepm*hstepm*stepm' months (i.e. until
+ #ifdef DEBUG
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
-      nhstepm*hstepm matrices.
+       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+ #endif
-      (typically every 2 years instead of every month which is too big
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-      for the memory).
+ }
-      Model is determined by parameters x and covariates have to be
-      included manually here.
+ /*************** linmin ************************/
+ /* 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
-   int i, j, d, h, k;
+ the value of func at the returned location p . This is actually all accomplished by calling the
-   double **out, cov[NCOVMAX];
+ routines mnbrak and brent .*/
-   double **newm;
+ int ncom;
+ double *pcom,*xicom;
-   /* Hstepm could be zero and should return the unit matrix */
+ double (*nrfunc)(double []);
-   for (i=1;i<=nlstate+ndeath;i++)
-     for (j=1;j<=nlstate+ndeath;j++){
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+ {
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+   double brent(double ax, double bx, double cx,
-     }
+                double (*f)(double), double tol, double *xmin);
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   double f1dim(double x);
-   for(h=1; h <=nhstepm; h++){
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-     for(d=1; d <=hstepm; d++){
+               double *fc, double (*func)(double));
-       newm=savm;
+   int j;
-       /* Covariates have to be included here again */
+   double xx,xmin,bx,ax;
-       cov[1]=1.;
+   double fx,fb,fa;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ #ifdef LINMINORIGINAL
-       for (k=1; k<=cptcovage;k++)
+ #else
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   double scale=10., axs, xxs; /* Scale added for infinity */
-       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]]];
+   ncom=n;
+   pcom=vector(1,n);
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+   xicom=vector(1,n);
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+   nrfunc=func;
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+   for (j=1;j<=n;j++) {
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+     pcom[j]=p[j];
-       savm=oldm;
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
-       oldm=newm;
+   }
-     }
-     for(i=1; i<=nlstate+ndeath; i++)
+ #ifdef LINMINORIGINAL
-       for(j=1;j<=nlstate+ndeath;j++) {
+   xx=1.;
-         po[i][j][h]=newm[i][j];
+ #else
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   axs=0.0;
-          */
+   xxs=1.;
-       }
+   do{
-   } /* end h */
+     xx= xxs;
-   return po;
+ #endif
- }
+     ax=0.;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
- /*************** log-likelihood *************/
+     /* 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))   */
- double func( double *x)
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
- {
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
-   int i, ii, j, k, mi, d, kk;
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+     /* 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]]*/
-   double **out;
+ #ifdef LINMINORIGINAL
-   double sw; /* Sum of weights */
+ #else
-   double lli; /* Individual log likelihood */
+     if (fx != fx){
-   int s1, s2;
+         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-   double bbh, survp;
+         printf("|");
-   long ipmx;
+         fprintf(ficlog,"|");
-   /*extern weight */
+ #ifdef DEBUGLINMIN
-   /* We are differentiating ll according to initial status */
+         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);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ #endif
-   /*for(i=1;i<imx;i++)
+     }
-     printf(" %d\n",s[4][i]);
+   }while(fx != fx);
-   */
+ #endif
-   cov[1]=1.;
+ #ifdef DEBUGLINMIN
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
-   if(mle==1){
+ #endif
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
-       for(mi=1; mi<= wav[i]-1; mi++){
+   /* fmin = f(p[j] + xmin * xi[j]) */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
-           for (j=1;j<=nlstate+ndeath;j++){
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef DEBUG
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-           }
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-         for(d=0; d<dh[mi][i]; d++){
+ #endif
-           newm=savm;
+ #ifdef DEBUGLINMIN
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   printf("linmin end ");
-           for (kk=1; kk<=cptcovage;kk++) {
+   fprintf(ficlog,"linmin end ");
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #endif
-           }
+   for (j=1;j<=n;j++) {
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ #ifdef LINMINORIGINAL
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     xi[j] *= xmin;
-           savm=oldm;
+ #else
-           oldm=newm;
+ #ifdef DEBUGLINMIN
-         } /* end mult */
+     if(xxs <1.0)
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+ #endif
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     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) */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+ #ifdef DEBUGLINMIN
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+     if(xxs <1.0)
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+       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 );
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+ #endif
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+ #endif
-          * probability in order to take into account the bias as a fraction of the way
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+   }
-          * -stepm/2 to stepm/2 .
+ #ifdef DEBUGLINMIN
-          * For stepm=1 the results are the same as for previous versions of Imach.
+   printf("\n");
-          * For stepm > 1 the results are less biased than in previous versions.
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-          */
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-         s1=s[mw[mi][i]][i];
+   for (j=1;j<=n;j++) {
-         s2=s[mw[mi+1][i]][i];
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-         bbh=(double)bh[mi][i]/(double)stepm;
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-         /* bias bh is positive if real duration
+     if(j % ncovmodel == 0){
-          * is higher than the multiple of stepm and negative otherwise.
+       printf("\n");
-          */
+       fprintf(ficlog,"\n");
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+     }
-         if( s2 > nlstate){
+   }
-           /* i.e. if s2 is a death state and if the date of death is known
+ #else
-              then the contribution to the likelihood is the probability to
+ #endif
-              die between last step unit time and current  step unit time,
+   free_vector(xicom,1,n);
-              which is also equal to probability to die before dh
+   free_vector(pcom,1,n);
-              minus probability to die before dh-stepm .
+ }
-              In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
-         health state: the date of the interview describes the actual state
+ /*************** powell ************************/
-         and not the date of a change in health state. The former idea was
+ /*
-         to consider that at each interview the state was recorded
+ Minimization of a function func of n variables. Input consists of an initial starting point
-         (healthy, disable or death) and IMaCh was corrected; but when we
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-         introduced the exact date of death then we should have modified
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-         the contribution of an exact death to the likelihood. This new
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-         contribution is smaller and very dependent of the step unit
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-         stepm. It is no more the probability to die between last interview
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-         and month of death but the probability to survive from last
+  */
-         interview up to one month before death multiplied by the
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         probability to die within a month. Thanks to Chris
+             double (*func)(double []))
-         Jackson for correcting this bug.  Former versions increased
+ {
-         mortality artificially. The bad side is that we add another loop
+   void linmin(double p[], double xi[], int n, double *fret,
-         which slows down the processing. The difference can be up to 10%
+               double (*func)(double []));
-         lower mortality.
+   int i,ibig,j;
-           */
+   double del,t,*pt,*ptt,*xit;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   double directest;
+   double fp,fptt;
+   double *xits;
-         } else if  (s2==-2) {
+   int niterf, itmp;
-           for (j=1,survp=0. ; j<=nlstate; j++)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   pt=vector(1,n);
-           /*survp += out[s1][j]; */
+   ptt=vector(1,n);
-           lli= log(survp);
+   xit=vector(1,n);
-         }
+   xits=vector(1,n);
+   *fret=(*func)(p);
-         else if  (s2==-4) {
+   for (j=1;j<=n;j++) pt[j]=p[j];
-           for (j=3,survp=0. ; j<=nlstate; j++)
+   rcurr_time = time(NULL);
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   for (*iter=1;;++(*iter)) {
-           lli= log(survp);
+     fp=(*fret); /* From former iteration or initial value */
-         }
+     ibig=0;
+     del=0.0;
-         else if  (s2==-5) {
+     rlast_time=rcurr_time;
-           for (j=1,survp=0. ; j<=2; j++)
+     /* (void) gettimeofday(&curr_time,&tzp); */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     rcurr_time = time(NULL);
-           lli= log(survp);
+     curr_time = *localtime(&rcurr_time);
-         }
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-         else{
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+     for (i=1;i<=n;i++) {
-           /*  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(" %d %.12f",i, p[i]);
-         }
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       fprintf(ficrespow," %.12lf", p[i]);
-         /*if(lli ==000.0)*/
+     }
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+     printf("\n");
-         ipmx +=1;
+     fprintf(ficlog,"\n");
-         sw += weight[i];
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     if(*iter <=3){
-       } /* end of wave */
+       tml = *localtime(&rcurr_time);
-     } /* end of individual */
+       strcpy(strcurr,asctime(&tml));
-   }  else if(mle==2){
+       rforecast_time=rcurr_time;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       itmp = strlen(strcurr);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       for(mi=1; mi<= wav[i]-1; mi++){
+         strcurr[itmp-1]='\0';
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-           for (j=1;j<=nlstate+ndeath;j++){
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(niterf=10;niterf<=30;niterf+=10){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-           }
+         forecast_time = *localtime(&rforecast_time);
-         for(d=0; d<=dh[mi][i]; d++){
+         strcpy(strfor,asctime(&forecast_time));
-           newm=savm;
+         itmp = strlen(strfor);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         if(strfor[itmp-1]=='\n')
-           for (kk=1; kk<=cptcovage;kk++) {
+         strfor[itmp-1]='\0';
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         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);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
+     for (i=1;i<=n;i++) { /* For each direction i */
-           oldm=newm;
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-         } /* end mult */
+       fptt=(*fret);
+ #ifdef DEBUG
-         s1=s[mw[mi][i]][i];
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         s2=s[mw[mi+1][i]][i];
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         bbh=(double)bh[mi][i]/(double)stepm;
+ #endif
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-         ipmx +=1;
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-         sw += weight[i];
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
-       } /* end of wave */
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-     } /* end of individual */
+         /* because that direction will be replaced unless the gain del is small */
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         /* with the new direction. */
-       for(mi=1; mi<= wav[i]-1; mi++){
+         del=fabs(fptt-(*fret));
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         ibig=i;
-           for (j=1;j<=nlstate+ndeath;j++){
+       }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef DEBUG
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       printf("%d %.12e",i,(*fret));
-           }
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-         for(d=0; d<dh[mi][i]; d++){
+       for (j=1;j<=n;j++) {
-           newm=savm;
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         printf(" x(%d)=%.12e",j,xit[j]);
-           for (kk=1; kk<=cptcovage;kk++) {
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       }
-           }
+       for(j=1;j<=n;j++) {
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         printf(" p(%d)=%.12e",j,p[j]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-           savm=oldm;
+       }
-           oldm=newm;
+       printf("\n");
-         } /* end mult */
+       fprintf(ficlog,"\n");
+ #endif
-         s1=s[mw[mi][i]][i];
+     } /* end loop on each direction i */
-         s2=s[mw[mi+1][i]][i];
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-         bbh=(double)bh[mi][i]/(double)stepm;
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-         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 */
+     /* New value of last point Pn is not computed, P(n-1) */
-         ipmx +=1;
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-         sw += weight[i];
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
-       } /* end of wave */
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
-     } /* end of individual */
+       /* decreased of more than 3.84  */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* By adding 10 parameters more the gain should be 18.31 */
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* Starting the program with initial values given by a former maximization will simply change */
-           for (j=1;j<=nlstate+ndeath;j++){
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
-           }
+ #ifdef DEBUG
-         for(d=0; d<dh[mi][i]; d++){
+       int k[2],l;
-           newm=savm;
+       k[0]=1;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       k[1]=-1;
-           for (kk=1; kk<=cptcovage;kk++) {
+       printf("Max: %.12e",(*func)(p));
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-           }
+       for (j=1;j<=n;j++) {
+         printf(" %.12e",p[j]);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         fprintf(ficlog," %.12e",p[j]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       }
-           savm=oldm;
+       printf("\n");
-           oldm=newm;
+       fprintf(ficlog,"\n");
-         } /* end mult */
+       for(l=0;l<=1;l++) {
+         for (j=1;j<=n;j++) {
-         s1=s[mw[mi][i]][i];
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-         s2=s[mw[mi+1][i]][i];
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-         if( s2 > nlstate){
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-           lli=log(out[s1][s2] - savm[s1][s2]);
+         }
-         }else{
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         }
+       }
-         ipmx +=1;
+ #endif
-         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]); */
+       free_vector(xit,1,n);
-       } /* end of wave */
+       free_vector(xits,1,n);
-     } /* end of individual */
+       free_vector(ptt,1,n);
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+       free_vector(pt,1,n);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       return;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     } /* enough precision */
-       for(mi=1; mi<= wav[i]-1; mi++){
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-           for (j=1;j<=nlstate+ndeath;j++){
+       ptt[j]=2.0*p[j]-pt[j];
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       xit[j]=p[j]-pt[j];
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       pt[j]=p[j];
-           }
+     }
-         for(d=0; d<dh[mi][i]; d++){
+     fptt=(*func)(ptt); /* f_3 */
-           newm=savm;
+ #ifdef POWELLF1F3
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #else
-           for (kk=1; kk<=cptcovage;kk++) {
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #endif
-           }
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-           savm=oldm;
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-           oldm=newm;
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-         } /* end mult */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+ #ifdef NRCORIGINAL
-         s1=s[mw[mi][i]][i];
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-         s2=s[mw[mi+1][i]][i];
+ #else
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
-         ipmx +=1;
+       t= t- del*SQR(fp-fptt);
-         sw += weight[i];
+ #endif
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+ #ifdef DEBUG
-       } /* end of wave */
+       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);
-     } /* end of individual */
+       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);
-   } /* End of if */
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-   return -l;
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
- }
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+ #endif
- /*************** log-likelihood *************/
+ #ifdef POWELLORIGINAL
- double funcone( double *x)
+       if (t < 0.0) { /* Then we use it for new direction */
- {
+ #else
-   /* Same as likeli but slower because of a lot of printf and if */
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-   int i, ii, j, k, mi, d, kk;
+         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);
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-   double **out;
+         fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
-   double lli; /* Individual log likelihood */
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-   double llt;
+       }
-   int s1, s2;
+       if (directest < 0.0) { /* Then we use it for new direction */
-   double bbh, survp;
+ #endif
-   /*extern weight */
+ #ifdef DEBUGLINMIN
-   /* We are differentiating ll according to initial status */
+         printf("Before linmin in direction P%d-P0\n",n);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         for (j=1;j<=n;j++) {
-   /*for(i=1;i<imx;i++)
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-     printf(" %d\n",s[4][i]);
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-   */
+           if(j % ncovmodel == 0){
-   cov[1]=1.;
+             printf("\n");
+             fprintf(ficlog,"\n");
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+           }
+         }
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #endif
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-     for(mi=1; mi<= wav[i]-1; mi++){
+ #ifdef DEBUGLINMIN
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=n;j++) {
-         for (j=1;j<=nlstate+ndeath;j++){
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           if(j % ncovmodel == 0){
-         }
+             printf("\n");
-       for(d=0; d<dh[mi][i]; d++){
+             fprintf(ficlog,"\n");
-         newm=savm;
+           }
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         }
-         for (kk=1; kk<=cptcovage;kk++) {
+ #endif
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         for (j=1;j<=n;j++) {
-         }
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         }
-         savm=oldm;
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-         oldm=newm;
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-       } /* end mult */
+ #ifdef DEBUG
-       s1=s[mw[mi][i]][i];
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       s2=s[mw[mi+1][i]][i];
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       bbh=(double)bh[mi][i]/(double)stepm;
+         for(j=1;j<=n;j++){
-       /* bias is positive if real duration
+           printf(" %.12e",xit[j]);
-        * is higher than the multiple of stepm and negative otherwise.
+           fprintf(ficlog," %.12e",xit[j]);
-        */
+         }
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         printf("\n");
-         lli=log(out[s1][s2] - savm[s1][s2]);
+         fprintf(ficlog,"\n");
-       } else if  (s2==-2) {
+ #endif
-         for (j=1,survp=0. ; j<=nlstate; j++)
+       } /* end of t or directest negative */
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ #ifdef POWELLF1F3
-         lli= log(survp);
+ #else
-       }else if (mle==1){
+     } /* end if (fptt < fp)  */
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ #endif
-       } else if(mle==2){
+   } /* loop iteration */
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+ }
-       } else if(mle==3){  /* exponential inter-extrapolation */
-         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-         lli=log(out[s1][s2]); /* Original formula */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+ {
-         lli=log(out[s1][s2]); /* Original formula */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-       } /* End of if */
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-       ipmx +=1;
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-       sw += weight[i];
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /* or prevalence in state 1, prevalence in state 2, 0 */
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-       if(globpr){
+   /* Initial matrix pimij */
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-  %11.6f %11.6f %11.6f ", \
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+   /*  0,                   0                  , 1} */
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+   /*
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+    * and after some iteration: */
-           llt +=ll[k]*gipmx/gsw;
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-         }
+   /*  0,                   0                  , 1} */
-         fprintf(ficresilk," %10.6f\n", -llt);
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-       }
+   /* {0.51571254859325999, 0.4842874514067399, */
-     } /* end of wave */
+   /*  0.51326036147820708, 0.48673963852179264} */
-   } /* end of individual */
+   /* If we start from prlim again, prlim tends to a constant matrix */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   int i, ii,j,k;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-   if(globpr==0){ /* First time we count the contributions and weights */
+   /* double **matprod2(); */ /* test */
-     gipmx=ipmx;
+   double **out, cov[NCOVMAX+1], **pmij();
-     gsw=sw;
+   double **newm;
-   }
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-   return -l;
+   int ncvloop=0;
- }
+   min=vector(1,nlstate);
+   max=vector(1,nlstate);
- /*************** function likelione ***********/
+   meandiff=vector(1,nlstate);
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
- {
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-   /* This routine should help understanding what is done with
+     for (j=1;j<=nlstate+ndeath;j++){
-      the selection of individuals/waves and
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-      to check the exact contribution to the likelihood.
+     }
-      Plotting could be done.
-    */
+   cov[1]=1.;
-   int k;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-     strcpy(fileresilk,"ilk");
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-     strcat(fileresilk,fileres);
+     ncvloop++;
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+     newm=savm;
-       printf("Problem with resultfile: %s\n", fileresilk);
+     /* Covariates have to be included here again */
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     cov[2]=agefin;
-     }
+     if(nagesqr==1)
-     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");
+       cov[3]= agefin*agefin;;
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     for (k=1; k<=cptcovn;k++) {
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-     for(k=1; k<=nlstate; k++)
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",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])]); */
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+     }
-   }
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-   *fretone=(*funcone)(p);
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
-   if(*globpri !=0){
+     for (k=1; k<=cptcovprod;k++) /* Useless */
-     fclose(ficresilk);
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-     fflush(fichtm);
-   }
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-   return;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- }
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
- /*********** Maximum Likelihood Estimation ***************/
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+     savm=oldm;
- {
+     oldm=newm;
-   int i,j, iter;
-   double **xi;
+     for(j=1; j<=nlstate; j++){
-   double fret;
+       max[j]=0.;
-   double fretone; /* Only one call to likelihood */
+       min[j]=1.;
-   /*  char filerespow[FILENAMELENGTH];*/
+     }
-   xi=matrix(1,npar,1,npar);
+     for(i=1;i<=nlstate;i++){
-   for (i=1;i<=npar;i++)
+       sumnew=0;
-     for (j=1;j<=npar;j++)
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+       for(j=1; j<=nlstate; j++){
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-   strcpy(filerespow,"pow");
+         max[j]=FMAX(max[j],prlim[i][j]);
-   strcat(filerespow,fileres);
+         min[j]=FMIN(min[j],prlim[i][j]);
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       }
-     printf("Problem with resultfile: %s\n", filerespow);
+     }
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   }
+     maxmax=0.;
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     for(j=1; j<=nlstate; j++){
-   for (i=1;i<=nlstate;i++)
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
-     for(j=1;j<=nlstate+ndeath;j++)
+       maxmax=FMAX(maxmax,meandiff[j]);
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
-   fprintf(ficrespow,"\n");
+     } /* j loop */
+     *ncvyear= (int)age- (int)agefin;
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
+     if(maxmax < ftolpl){
-   free_matrix(xi,1,npar,1,npar);
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
-   fclose(ficrespow);
+       free_vector(min,1,nlstate);
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+       free_vector(max,1,nlstate);
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       free_vector(meandiff,1,nlstate);
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       return prlim;
+     }
- }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
- /**** Computes Hessian and covariance matrix ***/
+   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\
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
- {
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
-   double  **a,**y,*x,pd;
+   free_vector(min,1,nlstate);
-   double **hess;
+   free_vector(max,1,nlstate);
-   int i, j,jk;
+   free_vector(meandiff,1,nlstate);
-   int *indx;
+   return prlim; /* should not reach here */
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+ }
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+ /*************** transition probabilities ***************/
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   double gompertz(double p[]);
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-   hess=matrix(1,npar,1,npar);
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+      computes the probability to be observed in state j being in state i by appying the
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+      model to the ncovmodel covariates (including constant and age).
-   for (i=1;i<=npar;i++){
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-     printf("%d",i);fflush(stdout);
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-     /*  printf(" %f ",p[i]);
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-   }
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
-   for (i=1;i<=npar;i++) {
+   double s1, lnpijopii;
-     for (j=1;j<=npar;j++)  {
+   /*double t34;*/
-       if (j>i) {
+   int i,j, nc, ii, jj;
-         printf(".%d%d",i,j);fflush(stdout);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+     for(i=1; i<= nlstate; i++){
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       for(j=1; j<i;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         hess[j][i]=hess[i][j];
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         /*printf(" %lf ",hess[i][j]);*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-       }
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     }
+         }
-   }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   printf("\n");
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   fprintf(ficlog,"\n");
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-   a=matrix(1,npar,1,npar);
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-   y=matrix(1,npar,1,npar);
+         }
-   x=vector(1,npar);
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   indx=ivector(1,npar);
+       }
-   for (i=1;i<=npar;i++)
+     }
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   ludcmp(a,npar,indx,&pd);
+     for(i=1; i<= nlstate; i++){
+       s1=0;
-   for (j=1;j<=npar;j++) {
+       for(j=1; j<i; j++){
-     for (i=1;i<=npar;i++) x[i]=0;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-     x[j]=1;
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-     lubksb(a,npar,indx,x);
+       }
-     for (i=1;i<=npar;i++){
+       for(j=i+1; j<=nlstate+ndeath; j++){
-       matcov[i][j]=x[i];
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-     }
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   }
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-   printf("\n#Hessian matrix#\n");
+       ps[i][i]=1./(s1+1.);
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+       /* Computing other pijs */
-   for (i=1;i<=npar;i++) {
+       for(j=1; j<i; j++)
-     for (j=1;j<=npar;j++) {
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       printf("%.3e ",hess[i][j]);
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     }
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-     printf("\n");
+     } /* end i */
-     fprintf(ficlog,"\n");
-   }
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-   /* Recompute Inverse */
+         ps[ii][jj]=0;
-   for (i=1;i<=npar;i++)
+         ps[ii][ii]=1;
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+       }
-   ludcmp(a,npar,indx,&pd);
+     }
-   /*  printf("\n#Hessian matrix recomputed#\n");
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-   for (j=1;j<=npar;j++) {
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-     for (i=1;i<=npar;i++) x[i]=0;
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-     x[j]=1;
+     /*   } */
-     lubksb(a,npar,indx,x);
+     /*   printf("\n "); */
-     for (i=1;i<=npar;i++){
+     /* } */
-       y[i][j]=x[i];
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-       printf("%.3e ",y[i][j]);
+     /*
-       fprintf(ficlog,"%.3e ",y[i][j]);
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-     }
+       goto end;*/
-     printf("\n");
+     return ps;
-     fprintf(ficlog,"\n");
+ }
-   }
-   */
+ /**************** Product of 2 matrices ******************/
-   free_matrix(a,1,npar,1,npar);
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-   free_matrix(y,1,npar,1,npar);
+ {
-   free_vector(x,1,npar);
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-   free_ivector(indx,1,npar);
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-   free_matrix(hess,1,npar,1,npar);
+   /* in, b, out are matrice of pointers which should have been initialized
+      before: only the contents of out is modified. The function returns
+      a pointer to pointers identical to out */
- }
+   int i, j, k;
+   for(i=nrl; i<= nrh; i++)
- /*************** hessian matrix ****************/
+     for(k=ncolol; k<=ncoloh; k++){
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+       out[i][k]=0.;
- {
+       for(j=ncl; j<=nch; j++)
-   int i;
+         out[i][k] +=in[i][j]*b[j][k];
-   int l=1, lmax=20;
+     }
-   double k1,k2;
+   return out;
-   double p2[NPARMAX+1];
+ }
-   double res;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
+ /************* Higher Matrix Product ***************/
-   int k=0,kmax=10;
-   double l1;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ {
-   fx=func(x);
+   /* Computes the transition matrix starting at age 'age' over
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+      'nhstepm*hstepm*stepm' months (i.e. until
-   for(l=0 ; l <=lmax; l++){
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-     l1=pow(10,l);
+      nhstepm*hstepm matrices.
-     delts=delt;
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-     for(k=1 ; k <kmax; k=k+1){
+      (typically every 2 years instead of every month which is too big
-       delt = delta*(l1*k);
+      for the memory).
-       p2[theta]=x[theta] +delt;
+      Model is determined by parameters x and covariates have to be
-       k1=func(p2)-fx;
+      included manually here.
-       p2[theta]=x[theta]-delt;
-       k2=func(p2)-fx;
+      */
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
- #ifdef DEBUG
+   double **newm;
-       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);
+   double agexact;
-       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);
+   double agebegin, ageend;
- #endif
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   /* Hstepm could be zero and should return the unit matrix */
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+   for (i=1;i<=nlstate+ndeath;i++)
-         k=kmax;
+     for (j=1;j<=nlstate+ndeath;j++){
-       }
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         k=kmax; l=lmax*10.;
+     }
-       }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   for(h=1; h <=nhstepm; h++){
-         delts=delt;
+     for(d=1; d <=hstepm; d++){
-       }
+       newm=savm;
-     }
+       /* Covariates have to be included here again */
-   }
+       cov[1]=1.;
-   delti[theta]=delts;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-   return res;
+       cov[2]=agexact;
+       if(nagesqr==1)
- }
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++)
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
- {
+         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-   int i;
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-   int l=1, l1, lmax=20;
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   double k1,k2,k3,k4,res,fx;
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   double p2[NPARMAX+1];
+         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
-   int k;
+       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)];
-   fx=func(x);
+         /* 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<=2; k++) {
-     for (i=1;i<=npar;i++) p2[i]=x[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-     k1=func(p2)-fx;
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       savm=oldm;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       oldm=newm;
-     k2=func(p2)-fx;
+     }
+     for(i=1; i<=nlstate+ndeath; i++)
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       for(j=1;j<=nlstate+ndeath;j++) {
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         po[i][j][h]=newm[i][j];
-     k3=func(p2)-fx;
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     /*printf("h=%d ",h);*/
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   } /* end h */
-     k4=func(p2)-fx;
+ /*     printf("\n H=%d \n",h); */
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+   return po;
- #ifdef DEBUG
+ }
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ #ifdef NLOPT
- #endif
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-   }
+   double fret;
-   return res;
+   double *xt;
- }
+   int j;
+   myfunc_data *d2 = (myfunc_data *) pd;
- /************** Inverse of matrix **************/
+ /* xt = (p1-1); */
- void ludcmp(double **a, int n, int *indx, double *d)
+   xt=vector(1,n);
- {
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   int i,imax,j,k;
-   double big,dum,sum,temp;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-   double *vv;
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
+   printf("Function = %.12lf ",fret);
-   vv=vector(1,n);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   *d=1.0;
+   printf("\n");
-   for (i=1;i<=n;i++) {
+  free_vector(xt,1,n);
-     big=0.0;
+   return fret;
-     for (j=1;j<=n;j++)
+ }
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+ #endif
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     vv[i]=1.0/big;
+ /*************** log-likelihood *************/
-   }
+ double func( double *x)
-   for (j=1;j<=n;j++) {
+ {
-     for (i=1;i<j;i++) {
+   int i, ii, j, k, mi, d, kk;
-       sum=a[i][j];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   double **out;
-       a[i][j]=sum;
+   double sw; /* Sum of weights */
-     }
+   double lli; /* Individual log likelihood */
-     big=0.0;
+   int s1, s2;
-     for (i=j;i<=n;i++) {
+   double bbh, survp;
-       sum=a[i][j];
+   long ipmx;
-       for (k=1;k<j;k++)
+   double agexact;
-         sum -= a[i][k]*a[k][j];
+   /*extern weight */
-       a[i][j]=sum;
+   /* We are differentiating ll according to initial status */
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         big=dum;
+   /*for(i=1;i<imx;i++)
-         imax=i;
+     printf(" %d\n",s[4][i]);
-       }
+   */
-     }
-     if (j != imax) {
+   ++countcallfunc;
-       for (k=1;k<=n;k++) {
-         dum=a[imax][k];
+   cov[1]=1.;
-         a[imax][k]=a[j][k];
-         a[j][k]=dum;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-       }
-       *d = -(*d);
+   if(mle==1){
-       vv[imax]=vv[j];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     }
+       /* Computes the values of the ncovmodel covariates of the model
-     indx[j]=imax;
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-     if (j != n) {
+          to be observed in j being in i according to the model.
-       dum=1.0/(a[j][j]);
+        */
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-     }
+           cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   }
+       }
-   free_vector(vv,1,n);  /* Doesn't work */
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
- ;
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
- }
+          has been calculated etc */
+       for(mi=1; mi<= wav[i]-1; mi++){
- void lubksb(double **a, int n, int *indx, double b[])
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- {
+           for (j=1;j<=nlstate+ndeath;j++){
-   int i,ii=0,ip,j;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double sum;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   for (i=1;i<=n;i++) {
+         for(d=0; d<dh[mi][i]; d++){
-     ip=indx[i];
+           newm=savm;
-     sum=b[ip];
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     b[ip]=b[i];
+           cov[2]=agexact;
-     if (ii)
+           if(nagesqr==1)
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+             cov[3]= agexact*agexact;
-     else if (sum) ii=i;
+           for (kk=1; kk<=cptcovage;kk++) {
-     b[i]=sum;
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-   }
+           }
-   for (i=n;i>=1;i--) {
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     sum=b[i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+           savm=oldm;
-     b[i]=sum/a[i][i];
+           oldm=newm;
-   }
+         } /* end mult */
- }
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
- void pstamp(FILE *fichier)
+         /* But now since version 0.9 we anticipate for bias at large stepm.
- {
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+          * (in months) between two waves is not a multiple of stepm, we rounded to
- }
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
- /************ Frequencies ********************/
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
- 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[])
+          * probability in order to take into account the bias as a fraction of the way
- {  /* Some frequencies */
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+          * -stepm/2 to stepm/2 .
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+          * For stepm=1 the results are the same as for previous versions of Imach.
-   int first;
+          * For stepm > 1 the results are less biased than in previous versions.
-   double ***freq; /* Frequencies */
+          */
-   double *pp, **prop;
+         s1=s[mw[mi][i]][i];
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+         s2=s[mw[mi+1][i]][i];
-   char fileresp[FILENAMELENGTH];
+         bbh=(double)bh[mi][i]/(double)stepm;
+         /* bias bh is positive if real duration
-   pp=vector(1,nlstate);
+          * is higher than the multiple of stepm and negative otherwise.
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+          */
-   strcpy(fileresp,"p");
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-   strcat(fileresp,fileres);
+         if( s2 > nlstate){
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+           /* i.e. if s2 is a death state and if the date of death is known
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+              then the contribution to the likelihood is the probability to
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+              die between last step unit time and current  step unit time,
-     exit(0);
+              which is also equal to probability to die before dh
-   }
+              minus probability to die before dh-stepm .
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+              In version up to 0.92 likelihood was computed
-   j1=0;
+         as if date of death was unknown. Death was treated as any other
+         health state: the date of the interview describes the actual state
-   j=cptcoveff;
+         and not the date of a change in health state. The former idea was
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         to consider that at each interview the state was recorded
+         (healthy, disable or death) and IMaCh was corrected; but when we
-   first=1;
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
-   for(k1=1; k1<=j;k1++){
+         contribution is smaller and very dependent of the step unit
-     for(i1=1; i1<=ncodemax[k1];i1++){
+         stepm. It is no more the probability to die between last interview
-       j1++;
+         and month of death but the probability to survive from last
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         interview up to one month before death multiplied by the
-         scanf("%d", i);*/
+         probability to die within a month. Thanks to Chris
-       for (i=-5; i<=nlstate+ndeath; i++)
+         Jackson for correcting this bug.  Former versions increased
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+         mortality artificially. The bad side is that we add another loop
-           for(m=iagemin; m <= iagemax+3; m++)
+         which slows down the processing. The difference can be up to 10%
-             freq[i][jk][m]=0;
+         lower mortality.
+           */
-     for (i=1; i<=nlstate; i++)
+         /* If, at the beginning of the maximization mostly, the
-       for(m=iagemin; m <= iagemax+3; m++)
+            cumulative probability or probability to be dead is
-         prop[i][m]=0;
+            constant (ie = 1) over time d, the difference is equal to
+.  out[s1][3] = savm[s1][3]: probability, being at state
-       dateintsum=0;
+            s1 at precedent wave, to be dead a month before current
-       k2cpt=0;
+            wave is equal to probability, being at state s1 at
-       for (i=1; i<=imx; i++) {
+            precedent wave, to be dead at mont of the current
-         bool=1;
+            wave. Then the observed probability (that this person died)
-         if  (cptcovn>0) {
+            is null according to current estimated parameter. In fact,
-           for (z1=1; z1<=cptcoveff; z1++)
+            it should be very low but not zero otherwise the log go to
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+            infinity.
-               bool=0;
+         */
-         }
+ /* #ifdef INFINITYORIGINAL */
-         if (bool==1){
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-           for(m=firstpass; m<=lastpass; m++){
+ /* #else */
-             k2=anint[m][i]+(mint[m][i]/12.);
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+ /*          lli=log(mytinydouble); */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+ /*        else */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+ /* #endif */
-               if (m<lastpass) {
+             lli=log(out[s1][s2] - savm[s1][s2]);
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+         } else if  (s2==-2) {
-               }
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+           /*survp += out[s1][j]; */
-                 dateintsum=dateintsum+k2;
+           lli= log(survp);
-                 k2cpt++;
+         }
-               }
-               /*}*/
+         else if  (s2==-4) {
-           }
+           for (j=3,survp=0. ; j<=nlstate; j++)
-         }
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       }
+           lli= log(survp);
+         }
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
+         else if  (s2==-5) {
-       if  (cptcovn>0) {
+           for (j=1,survp=0. ; j<=2; j++)
-         fprintf(ficresp, "\n#********** Variable ");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+           lli= log(survp);
-         fprintf(ficresp, "**********\n#");
+         }
-       }
-       for(i=1; i<=nlstate;i++)
+         else{
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       fprintf(ficresp, "\n");
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+         }
-       for(i=iagemin; i <= iagemax+3; i++){
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         if(i==iagemax+3){
+         /*if(lli ==000.0)*/
-           fprintf(ficlog,"Total");
+         /*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); */
-         }else{
+         ipmx +=1;
-           if(first==1){
+         sw += weight[i];
-             first=0;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-             printf("See log file for details...\n");
+         /* if (lli < log(mytinydouble)){ */
-           }
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
-           fprintf(ficlog,"Age %d", i);
+         /*   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]); */
-         }
+         /* } */
-         for(jk=1; jk <=nlstate ; jk++){
+       } /* end of wave */
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+     } /* end of individual */
-             pp[jk] += freq[jk][m][i];
+   }  else if(mle==2){
-         }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         for(jk=1; jk <=nlstate ; jk++){
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-           for(m=-1, pos=0; m <=0 ; m++)
+       for(mi=1; mi<= wav[i]-1; mi++){
-             pos += freq[jk][m][i];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-           if(pp[jk]>=1.e-10){
+           for (j=1;j<=nlstate+ndeath;j++){
-             if(first==1){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-             }
+           }
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         for(d=0; d<=dh[mi][i]; d++){
-           }else{
+           newm=savm;
-             if(first==1)
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           cov[2]=agexact;
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           if(nagesqr==1)
-           }
+             cov[3]= agexact*agexact;
-         }
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-         for(jk=1; jk <=nlstate ; jk++){
+           }
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-             pp[jk] += freq[jk][m][i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         }
+           savm=oldm;
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+           oldm=newm;
-           pos += pp[jk];
+         } /* end mult */
-           posprop += prop[jk][i];
-         }
+         s1=s[mw[mi][i]][i];
-         for(jk=1; jk <=nlstate ; jk++){
+         s2=s[mw[mi+1][i]][i];
-           if(pos>=1.e-5){
+         bbh=(double)bh[mi][i]/(double)stepm;
-             if(first==1)
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         ipmx +=1;
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         sw += weight[i];
-           }else{
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-             if(first==1)
+       } /* end of wave */
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+     } /* end of individual */
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-           }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           if( i <= iagemax){
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-             if(pos>=1.e-5){
+       for(mi=1; mi<= wav[i]-1; mi++){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+           for (j=1;j<=nlstate+ndeath;j++){
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-             else
+           }
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+         for(d=0; d<dh[mi][i]; d++){
-           }
+           newm=savm;
-         }
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+           if(nagesqr==1)
-           for(m=-1; m <=nlstate+ndeath; m++)
+             cov[3]= agexact*agexact;
-             if(freq[jk][m][i] !=0 ) {
+           for (kk=1; kk<=cptcovage;kk++) {
-             if(first==1)
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+           }
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-             }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         if(i <= iagemax)
+           savm=oldm;
-           fprintf(ficresp,"\n");
+           oldm=newm;
-         if(first==1)
+         } /* end mult */
-           printf("Others in log...\n");
-         fprintf(ficlog,"\n");
+         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 */
-   dateintmean=dateintsum/k2cpt;
+         ipmx +=1;
+         sw += weight[i];
-   fclose(ficresp);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+       } /* end of wave */
-   free_vector(pp,1,nlstate);
+     } /* end of individual */
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   /* End of Freq */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- }
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
- /************ Prevalence ********************/
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+           for (j=1;j<=nlstate+ndeath;j++){
- {
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+           }
-      We still use firstpass and lastpass as another selection.
+         for(d=0; d<dh[mi][i]; d++){
-   */
+           newm=savm;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+           cov[2]=agexact;
-   double ***freq; /* Frequencies */
+           if(nagesqr==1)
-   double *pp, **prop;
+             cov[3]= agexact*agexact;
-   double pos,posprop;
+           for (kk=1; kk<=cptcovage;kk++) {
-   double  y2; /* in fractional years */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   int iagemin, iagemax;
+           }
-   iagemin= (int) agemin;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   iagemax= (int) agemax;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /*pp=vector(1,nlstate);*/
+           savm=oldm;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+           oldm=newm;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+         } /* end mult */
-   j1=0;
+         s1=s[mw[mi][i]][i];
-   j=cptcoveff;
+         s2=s[mw[mi+1][i]][i];
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         if( s2 > nlstate){
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   for(k1=1; k1<=j;k1++){
+         }else{
-     for(i1=1; i1<=ncodemax[k1];i1++){
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       j1++;
+         }
+         ipmx +=1;
-       for (i=1; i<=nlstate; i++)
+         sw += weight[i];
-         for(m=iagemin; m <= iagemax+3; m++)
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-           prop[i][m]=0.0;
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       } /* end of wave */
-       for (i=1; i<=imx; i++) { /* Each individual */
+     } /* end of individual */
-         bool=1;
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-         if  (cptcovn>0) {
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           for (z1=1; z1<=cptcoveff; z1++)
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+       for(mi=1; mi<= wav[i]-1; mi++){
-               bool=0;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         }
+           for (j=1;j<=nlstate+ndeath;j++){
-         if (bool==1) {
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+           }
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+         for(d=0; d<dh[mi][i]; d++){
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+           newm=savm;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+           cov[2]=agexact;
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+           if(nagesqr==1)
-                 /*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]]);*/
+             cov[3]= agexact*agexact;
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+           for (kk=1; kk<=cptcovage;kk++) {
-                 prop[s[m][i]][iagemax+3] += weight[i];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-               }
+           }
-             }
-           } /* end selection of waves */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       }
+           savm=oldm;
-       for(i=iagemin; i <= iagemax+3; i++){
+           oldm=newm;
+         } /* end mult */
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-           posprop += prop[jk][i];
+         s1=s[mw[mi][i]][i];
-         }
+         s2=s[mw[mi+1][i]][i];
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         for(jk=1; jk <=nlstate ; jk++){
+         ipmx +=1;
-           if( i <=  iagemax){
+         sw += weight[i];
-             if(posprop>=1.e-5){
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-             }
+       } /* end of wave */
-           }
+     } /* end of individual */
-         }/* end jk */
+   } /* End of if */
-       }/* end i */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     } /* end i1 */
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   } /* end k1 */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
-   /*  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);
+ /*************** log-likelihood *************/
- }  /* End of prevalence */
+ double funcone( double *x)
+ {
- /************* Waves Concatenation ***************/
+   /* Same as likeli but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
- 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)
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
- {
+   double **out;
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   double lli; /* Individual log likelihood */
-      Death is a valid wave (if date is known).
+   double llt;
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+   int s1, s2;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+   double bbh, survp;
-      and mw[mi+1][i]. dh depends on stepm.
+   double agexact;
-      */
+   double agebegin, ageend;
+   /*extern weight */
-   int i, mi, m;
+   /* We are differentiating ll according to initial status */
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-      double sum=0., jmean=0.;*/
+   /*for(i=1;i<imx;i++)
-   int first;
+     printf(" %d\n",s[4][i]);
-   int j, k=0,jk, ju, jl;
+   */
-   double sum=0.;
+   cov[1]=1.;
-   first=0;
-   jmin=1e+5;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   jmax=-1;
-   jmean=0.;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   for(i=1; i<=imx; i++){
+     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-     mi=0;
+     for(mi=1; mi<= wav[i]-1; mi++){
-     m=firstpass;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-     while(s[m][i] <= nlstate){
+         for (j=1;j<=nlstate+ndeath;j++){
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         mw[++mi][i]=m;
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       if(m >=lastpass)
+         }
-         break;
-       else
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
-         m++;
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
-     }/* end while */
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-     if (s[m][i] > nlstate){
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-       mi++;     /* Death is another wave */
+           and mw[mi+1][i]. dh depends on stepm.*/
-       /* if(mi==0)  never been interviewed correctly before death */
+         newm=savm;
-          /* Only death is a correct wave */
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       mw[mi][i]=m;
+         cov[2]=agexact;
-     }
+         if(nagesqr==1)
+           cov[3]= agexact*agexact;
-     wav[i]=mi;
+         for (kk=1; kk<=cptcovage;kk++) {
-     if(mi==0){
+           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-       nbwarn++;
+         }
-       if(first==0){
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         first=1;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       if(first==1){
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-       }
+         savm=oldm;
-     } /* end mi==0 */
+         oldm=newm;
-   } /* End individuals */
+       } /* end mult */
-   for(i=1; i<=imx; i++){
+       s1=s[mw[mi][i]][i];
-     for(mi=1; mi<wav[i];mi++){
+       s2=s[mw[mi+1][i]][i];
-       if (stepm <=0)
+       bbh=(double)bh[mi][i]/(double)stepm;
-         dh[mi][i]=1;
+       /* bias is positive if real duration
-       else{
+        * is higher than the multiple of stepm and negative otherwise.
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+        */
-           if (agedc[i] < 2*AGESUP) {
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+         lli=log(out[s1][s2] - savm[s1][s2]);
-             if(j==0) j=1;  /* Survives at least one month after exam */
+       } else if  (s2==-2) {
-             else if(j<0){
+         for (j=1,survp=0. ; j<=nlstate; j++)
-               nberr++;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-               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]);
+         lli= log(survp);
-               j=1; /* Temporary Dangerous patch */
+       }else if (mle==1){
-               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);
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-               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]);
+       } else if(mle==2){
-               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);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-             }
+       } else if(mle==3){  /* exponential inter-extrapolation */
-             k=k+1;
+         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 (j >= jmax){
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-               jmax=j;
+         lli=log(out[s1][s2]); /* Original formula */
-               ijmax=i;
+       } else{  /* mle=0 back to 1 */
-             }
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-             if (j <= jmin){
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-               jmin=j;
+       } /* End of if */
-               ijmin=i;
+       ipmx +=1;
-             }
+       sw += weight[i];
-             sum=sum+j;
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-             /*if (j<0) printf("j=%d num=%d \n",j,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]); */
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+       if(globpr){
-           }
+         fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
-         }
+  %11.6f %11.6f %11.6f ", \
-         else{
+                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
- /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
-           k=k+1;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-           if (j >= jmax) {
+         }
-             jmax=j;
+         fprintf(ficresilk," %10.6f\n", -llt);
-             ijmax=i;
+       }
-           }
+     } /* end of wave */
-           else if (j <= jmin){
+   } /* end of individual */
-             jmin=j;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-             ijmin=i;
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-           }
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   if(globpr==0){ /* First time we count the contributions and weights */
-           /*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]);*/
+     gipmx=ipmx;
-           if(j<0){
+     gsw=sw;
-             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]);
+   return -l;
-             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]);
+ }
-           }
-           sum=sum+j;
-         }
+ /*************** function likelione ***********/
-         jk= j/stepm;
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-         jl= j -jk*stepm;
+ {
-         ju= j -(jk+1)*stepm;
+   /* This routine should help understanding what is done with
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+      the selection of individuals/waves and
-           if(jl==0){
+      to check the exact contribution to the likelihood.
-             dh[mi][i]=jk;
+      Plotting could be done.
-             bh[mi][i]=0;
+    */
-           }else{ /* We want a negative bias in order to only have interpolation ie
+   int k;
-                   * at the price of an extra matrix product in likelihood */
-             dh[mi][i]=jk+1;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-             bh[mi][i]=ju;
+     strcpy(fileresilk,"ILK_");
-           }
+     strcat(fileresilk,fileresu);
-         }else{
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-           if(jl <= -ju){
+       printf("Problem with resultfile: %s\n", fileresilk);
-             dh[mi][i]=jk;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-             bh[mi][i]=jl;       /* bias is positive if real duration
+     }
-                                  * is higher than the multiple of stepm and negative otherwise.
+     fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-                                  */
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
-           }
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-           else{
+     for(k=1; k<=nlstate; k++)
-             dh[mi][i]=jk+1;
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-             bh[mi][i]=ju;
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-           }
+   }
-           if(dh[mi][i]==0){
-             dh[mi][i]=1; /* At least one step */
+   *fretone=(*funcone)(p);
-             bh[mi][i]=ju; /* At least one step */
+   if(*globpri !=0){
-             /*  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);*/
+     fclose(ficresilk);
-           }
+     if (mle ==0)
-         } /* end if mle */
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-       }
+     else if(mle >=1)
-     } /* end wave */
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
-   }
+     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   jmean=sum/k;
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+     for (k=1; k<= nlstate ; k++) {
-  }
+       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
- /*********** Tricode ****************************/
+     }
- void tricode(int *Tvar, int **nbcode, int imx)
+     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
- {
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-   int cptcode=0;
+     fflush(fichtm);
-   cptcoveff=0;
+   }
+   return;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+ }
-   for (k=1; k<=7; k++) ncodemax[k]=0;
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+ /*********** Maximum Likelihood Estimation ***************/
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
-                                modality*/
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+ {
-       Ndum[ij]++; /*store the modality */
+   int i,j, iter=0;
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+   double **xi;
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+   double fret;
-                                        Tvar[j]. If V=sex and male is 0 and
+   double fretone; /* Only one call to likelihood */
-                                        female is 1, then  cptcode=1.*/
+   /*  char filerespow[FILENAMELENGTH];*/
-     }
+ #ifdef NLOPT
-     for (i=0; i<=cptcode; i++) {
+   int creturn;
-       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 */
+   nlopt_opt opt;
-     }
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
+   double *lb;
-     ij=1;
+   double minf; /* the minimum objective value, upon return */
-     for (i=1; i<=ncodemax[j]; i++) {
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-       for (k=0; k<= maxncov; k++) {
+   myfunc_data dinst, *d = &dinst;
-         if (Ndum[k] != 0) {
+ #endif
-           nbcode[Tvar[j]][ij]=k;
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+   xi=matrix(1,npar,1,npar);
-           ij++;
+   for (i=1;i<=npar;i++)
-         }
+     for (j=1;j<=npar;j++)
-         if (ij > ncodemax[j]) break;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-       }
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     }
+   strcpy(filerespow,"POW_");
-   }
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+     printf("Problem with resultfile: %s\n", filerespow);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-  for (i=1; i<=ncovmodel-2; i++) {
+   }
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-    ij=Tvar[i];
+   for (i=1;i<=nlstate;i++)
-    Ndum[ij]++;
+     for(j=1;j<=nlstate+ndeath;j++)
-  }
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   fprintf(ficrespow,"\n");
-  ij=1;
+ #ifdef POWELL
-  for (i=1; i<= maxncov; i++) {
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+ #endif
-      Tvaraff[ij]=i; /*For printing */
-      ij++;
+ #ifdef NLOPT
-    }
+ #ifdef NEWUOA
-  }
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
-  cptcoveff=ij-1; /*Number of simple covariates*/
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
- }
+ #endif
+   lb=vector(0,npar-1);
- /*********** Health Expectancies ****************/
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
- 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[] )
+   nlopt_set_initial_step1(opt, 0.1);
- {
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   /* Health expectancies, no variances */
+   d->function = func;
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   double age, agelim, hf;
+   nlopt_set_min_objective(opt, myfunc, d);
-   double ***p3mat;
+   nlopt_set_xtol_rel(opt, ftol);
-   double eip;
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+     printf("nlopt failed! %d\n",creturn);
-   pstamp(ficreseij);
+   }
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   else {
-   fprintf(ficreseij,"# Age");
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   for(i=1; i<=nlstate;i++){
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-     for(j=1; j<=nlstate;j++){
+     iter=1; /* not equal */
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   }
-     }
+   nlopt_destroy(opt);
-     fprintf(ficreseij," e%1d. ",i);
+ #endif
-   }
+   free_matrix(xi,1,npar,1,npar);
-   fprintf(ficreseij,"\n");
+   fclose(ficrespow);
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   if(estepm < stepm){
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+ }
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+ /**** Computes Hessian and covariance matrix ***/
-    * This is mainly to measure the difference between two models: for example
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-    * 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
+   double  **a,**y,*x,pd;
-    * progression in between and thus overestimating or underestimating according
+   /* double **hess; */
-    * to the curvature of the survival function. If, for the same date, we
+   int i, j;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   int *indx;
-    * to compare the new estimate of Life expectancy with the same linear
-    * hypothesis. A more precise result, taking into account a more precise
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-    * curvature will be obtained if estepm is as small as stepm. */
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   double gompertz(double p[]);
-      nhstepm is the number of hstepm from age to agelim
+   /* hess=matrix(1,npar,1,npar); */
-      nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-      and note for a fixed period like estepm months */
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   for (i=1;i<=npar;i++){
-      survival function given by stepm (the optimization length). Unfortunately it
+     printf("%d-",i);fflush(stdout);
-      means that if the survival funtion is printed only each two years of age and if
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
-      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.
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-   agelim=AGESUP;
+   }
-   /* If stepm=6 months */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+   for (i=1;i<=npar;i++) {
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     for (j=1;j<=npar;j++)  {
+       if (j>i) {
- /* nhstepm age range expressed in number of stepm */
+         printf(".%d-%d",i,j);fflush(stdout);
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         hess[j][i]=hess[i][j];
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /*printf(" %lf ",hess[i][j]);*/
+       }
-   for (age=bage; age<=fage; age ++){
+     }
+   }
+   printf("\n");
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   fprintf(ficlog,"\n");
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-     printf("%d|",(int)age);fflush(stdout);
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   a=matrix(1,npar,1,npar);
+   y=matrix(1,npar,1,npar);
+   x=vector(1,npar);
-     /* Computing expectancies */
+   indx=ivector(1,npar);
-     for(i=1; i<=nlstate;i++)
+   for (i=1;i<=npar;i++)
-       for(j=1; j<=nlstate;j++)
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   ludcmp(a,npar,indx,&pd);
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+   for (j=1;j<=npar;j++) {
-           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+     for (i=1;i<=npar;i++) x[i]=0;
+     x[j]=1;
-         }
+     lubksb(a,npar,indx,x);
+     for (i=1;i<=npar;i++){
-     fprintf(ficreseij,"%3.0f",age );
+       matcov[i][j]=x[i];
-     for(i=1; i<=nlstate;i++){
+     }
-       eip=0;
+   }
-       for(j=1; j<=nlstate;j++){
-         eip +=eij[i][j][(int)age];
+   printf("\n#Hessian matrix#\n");
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-       }
+   for (i=1;i<=npar;i++) {
-       fprintf(ficreseij,"%9.4f", eip );
+     for (j=1;j<=npar;j++) {
-     }
+       printf("%.6e ",hess[i][j]);
-     fprintf(ficreseij,"\n");
+       fprintf(ficlog,"%.6e ",hess[i][j]);
+     }
-   }
+     printf("\n");
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     fprintf(ficlog,"\n");
-   printf("\n");
+   }
-   fprintf(ficlog,"\n");
+   /* printf("\n#Covariance matrix#\n"); */
- }
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
- 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 (j=1;j<=npar;j++) {  */
+   /*     printf("%.6e ",matcov[i][j]); */
- {
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
-   /* Covariances of health expectancies eij and of total life expectancies according
+   /*   } */
-    to initial status i, ei. .
+   /*   printf("\n"); */
-   */
+   /*   fprintf(ficlog,"\n"); */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   /* } */
-   double age, agelim, hf;
-   double ***p3matp, ***p3matm, ***varhe;
+   /* Recompute Inverse */
-   double **dnewm,**doldm;
+   /* for (i=1;i<=npar;i++) */
-   double *xp, *xm;
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   double **gp, **gm;
+   /* ludcmp(a,npar,indx,&pd); */
-   double ***gradg, ***trgradg;
-   int theta;
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
-   double eip, vip;
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   /*   x[j]=1; */
-   xp=vector(1,npar);
+   /*   lubksb(a,npar,indx,x); */
-   xm=vector(1,npar);
+   /*   for (i=1;i<=npar;i++){  */
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   /*     y[i][j]=x[i]; */
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
-   pstamp(ficresstdeij);
+   /*   } */
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   /*   printf("\n"); */
-   fprintf(ficresstdeij,"# Age");
+   /*   fprintf(ficlog,"\n"); */
-   for(i=1; i<=nlstate;i++){
+   /* } */
-     for(j=1; j<=nlstate;j++)
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   /* Verifying the inverse matrix */
-     fprintf(ficresstdeij," e%1d. ",i);
+ #ifdef DEBUGHESS
-   }
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-   fprintf(ficresstdeij,"\n");
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
-   pstamp(ficrescveij);
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-   fprintf(ficrescveij,"# Age");
+   for (j=1;j<=npar;j++) {
-   for(i=1; i<=nlstate;i++)
+     for (i=1;i<=npar;i++){
-     for(j=1; j<=nlstate;j++){
+       printf("%.2f ",y[i][j]);
-       cptj= (j-1)*nlstate+i;
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       for(i2=1; i2<=nlstate;i2++)
+     }
-         for(j2=1; j2<=nlstate;j2++){
+     printf("\n");
-           cptj2= (j2-1)*nlstate+i2;
+     fprintf(ficlog,"\n");
-           if(cptj2 <= cptj)
+   }
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+ #endif
-         }
-     }
+   free_matrix(a,1,npar,1,npar);
-   fprintf(ficrescveij,"\n");
+   free_matrix(y,1,npar,1,npar);
+   free_vector(x,1,npar);
-   if(estepm < stepm){
+   free_ivector(indx,1,npar);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   /* free_matrix(hess,1,npar,1,npar); */
-   }
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+ }
-    * 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
+ /*************** hessian matrix ****************/
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-    * progression in between and thus overestimating or underestimating according
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
-    * to the curvature of the survival function. If, for the same date, we
+   int i;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   int l=1, lmax=20;
-    * to compare the new estimate of Life expectancy with the same linear
+   double k1,k2, res, fx;
-    * hypothesis. A more precise result, taking into account a more precise
+   double p2[MAXPARM+1]; /* identical to x */
-    * curvature will be obtained if estepm is as small as stepm. */
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   int k=0,kmax=10;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   double l1;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
+   fx=func(x);
-      nstepm is the number of stepm from age to agelin.
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-      Look at hpijx to understand the reason of that which relies in memory size
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-      and note for a fixed period like estepm months */
+     l1=pow(10,l);
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     delts=delt;
-      survival function given by stepm (the optimization length). Unfortunately it
+     for(k=1 ; k <kmax; k=k+1){
-      means that if the survival funtion is printed only each two years of age and if
+       delt = delta*(l1*k);
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       p2[theta]=x[theta] +delt;
-      results. So we changed our mind and took the option of the best precision.
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   */
+       p2[theta]=x[theta]-delt;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       k2=func(p2)-fx;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   /* If stepm=6 months */
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
-   /* nhstepm age range expressed in number of stepm */
-   agelim=AGESUP;
+ #ifdef DEBUGHESSII
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       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);
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   /* if (stepm >= YEARM) hstepm=1;*/
+ #endif
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         k=kmax;
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+         k=kmax; l=lmax*10;
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+       }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+         delts=delt;
-   for (age=bage; age<=fage; age ++){
+       }
+     } /* End loop k */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+   }
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   delti[theta]=delts;
+   return res;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+ }
-     /* Computing  Variances of health expectancies */
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-        decrease memory allocation */
+ {
-     for(theta=1; theta <=npar; theta++){
+   int i;
-       for(i=1; i<=npar; i++){
+   int l=1, lmax=20;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   double k1,k2,k3,k4,res,fx;
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+   double p2[MAXPARM+1];
-       }
+   int k, kmax=1;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+   double v1, v2, cv12, lc1, lc2;
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+   int firstime=0;
-       for(j=1; j<= nlstate; j++){
-         for(i=1; i<=nlstate; i++){
+   fx=func(x);
-           for(h=0; h<=nhstepm-1; h++){
+   for (k=1; k<=kmax; k=k+10) {
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-           }
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-         }
+     k1=func(p2)-fx;
-       }
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-         for(h=0; h<=nhstepm-1; h++){
+     k2=func(p2)-fx;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         }
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     }/* End theta */
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
+     k3=func(p2)-fx;
-     for(h=0; h<=nhstepm-1; h++)
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-       for(j=1; j<=nlstate*nlstate;j++)
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-         for(theta=1; theta <=npar; theta++)
+     k4=func(p2)-fx;
-           trgradg[h][j][theta]=gradg[h][theta][j];
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
+     if(k1*k2*k3*k4 <0.){
+       firstime=1;
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+       kmax=kmax+10;
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+     }
-         varhe[ij][ji][(int)age] =0.;
+     if(kmax >=10 || firstime ==1){
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
-      printf("%d|",(int)age);fflush(stdout);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+       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(h=0;h<=nhstepm-1;h++){
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-       for(k=0;k<=nhstepm-1;k++){
+     }
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+ #ifdef DEBUGHESSIJ
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+     v1=hess[thetai][thetai];
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+     v2=hess[thetaj][thetaj];
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+     cv12=res;
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+     /* Computing eigen value of Hessian matrix */
-       }
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     }
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     if ((lc2 <0) || (lc1 <0) ){
-     /* Computing expectancies */
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-     for(i=1; i<=nlstate;i++)
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-       for(j=1; j<=nlstate;j++)
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+     }
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+ #endif
+   }
-           /* 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]);*/
+   return res;
+ }
-         }
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
-     fprintf(ficresstdeij,"%3.0f",age );
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
-     for(i=1; i<=nlstate;i++){
+ /* { */
-       eip=0.;
+ /*   int i; */
-       vip=0.;
+ /*   int l=1, lmax=20; */
-       for(j=1; j<=nlstate;j++){
+ /*   double k1,k2,k3,k4,res,fx; */
-         eip += eij[i][j][(int)age];
+ /*   double p2[MAXPARM+1]; */
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ /*   int k=0,kmax=10; */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ /*   double l1; */
-       }
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+ /*   fx=func(x); */
-     }
+ /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
-     fprintf(ficresstdeij,"\n");
+ /*     l1=pow(10,l); */
+ /*     delts=delt; */
-     fprintf(ficrescveij,"%3.0f",age );
+ /*     for(k=1 ; k <kmax; k=k+1){ */
-     for(i=1; i<=nlstate;i++)
+ /*       delt = delti*(l1*k); */
-       for(j=1; j<=nlstate;j++){
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
-         cptj= (j-1)*nlstate+i;
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-         for(i2=1; i2<=nlstate;i2++)
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-           for(j2=1; j2<=nlstate;j2++){
+ /*       k1=func(p2)-fx; */
-             cptj2= (j2-1)*nlstate+i2;
-             if(cptj2 <= cptj)
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-           }
+ /*       k2=func(p2)-fx; */
-       }
-     fprintf(ficrescveij,"\n");
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-   }
+ /*       k3=func(p2)-fx; */
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+ /*       k4=func(p2)-fx; */
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /* #ifdef DEBUGHESSIJ */
-   printf("\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,"\n");
+ /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+ /* #endif */
-   free_vector(xm,1,npar);
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
-   free_vector(xp,1,npar);
+ /*      k=kmax; */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+ /*       } */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+ /*       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_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+ /*      k=kmax; l=lmax*10; */
- }
+ /*       } */
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
- /************ Variance ******************/
+ /*      delts=delt; */
- 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[])
+ /*       } */
- {
+ /*     } /\* End loop k *\/ */
-   /* Variance of health expectancies */
+ /*   } */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+ /*   delti[theta]=delts; */
-   /* double **newm;*/
+ /*   return res;  */
-   double **dnewm,**doldm;
+ /* } */
-   double **dnewmp,**doldmp;
-   int i, j, nhstepm, hstepm, h, nstepm ;
-   int k, cptcode;
+ /************** Inverse of matrix **************/
-   double *xp;
+ void ludcmp(double **a, int n, int *indx, double *d)
-   double **gp, **gm;  /* for var eij */
+ {
-   double ***gradg, ***trgradg; /*for var eij */
+   int i,imax,j,k;
-   double **gradgp, **trgradgp; /* for var p point j */
+   double big,dum,sum,temp;
-   double *gpp, *gmp; /* for var p point j */
+   double *vv;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   double ***p3mat;
+   vv=vector(1,n);
-   double age,agelim, hf;
+   *d=1.0;
-   double ***mobaverage;
+   for (i=1;i<=n;i++) {
-   int theta;
+     big=0.0;
-   char digit[4];
+     for (j=1;j<=n;j++)
-   char digitp[25];
+       if ((temp=fabs(a[i][j])) > big) big=temp;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-   char fileresprobmorprev[FILENAMELENGTH];
+     vv[i]=1.0/big;
+   }
-   if(popbased==1){
+   for (j=1;j<=n;j++) {
-     if(mobilav!=0)
+     for (i=1;i<j;i++) {
-       strcpy(digitp,"-populbased-mobilav-");
+       sum=a[i][j];
-     else strcpy(digitp,"-populbased-nomobil-");
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-   }
+       a[i][j]=sum;
-   else
+     }
-     strcpy(digitp,"-stablbased-");
+     big=0.0;
+     for (i=j;i<=n;i++) {
-   if (mobilav!=0) {
+       sum=a[i][j];
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for (k=1;k<j;k++)
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         sum -= a[i][k]*a[k][j];
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       a[i][j]=sum;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-     }
+         big=dum;
-   }
+         imax=i;
+       }
-   strcpy(fileresprobmorprev,"prmorprev");
+     }
-   sprintf(digit,"%-d",ij);
+     if (j != imax) {
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+       for (k=1;k<=n;k++) {
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+         dum=a[imax][k];
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+         a[imax][k]=a[j][k];
-   strcat(fileresprobmorprev,fileres);
+         a[j][k]=dum;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+       }
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+       *d = -(*d);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+       vv[imax]=vv[j];
-   }
+     }
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     indx[j]=imax;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     if (j != n) {
-   pstamp(ficresprobmorprev);
+       dum=1.0/(a[j][j]);
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+     }
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   }
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   free_vector(vv,1,n);  /* Doesn't work */
-     for(i=1; i<=nlstate;i++)
+ ;
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+ }
-   }
-   fprintf(ficresprobmorprev,"\n");
+ void lubksb(double **a, int n, int *indx, double b[])
-   fprintf(ficgp,"\n# Routine varevsij");
+ {
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   int i,ii=0,ip,j;
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+   double sum;
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- /*   } */
+   for (i=1;i<=n;i++) {
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     ip=indx[i];
-   pstamp(ficresvij);
+     sum=b[ip];
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+     b[ip]=b[i];
-   if(popbased==1)
+     if (ii)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   else
+     else if (sum) ii=i;
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+     b[i]=sum;
-   fprintf(ficresvij,"# Age");
+   }
-   for(i=1; i<=nlstate;i++)
+   for (i=n;i>=1;i--) {
-     for(j=1; j<=nlstate;j++)
+     sum=b[i];
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-   fprintf(ficresvij,"\n");
+     b[i]=sum/a[i][i];
+   }
-   xp=vector(1,npar);
+ }
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
+ void pstamp(FILE *fichier)
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+ {
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
+ }
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+ /************ Frequencies ********************/
-   gmp=vector(nlstate+1,nlstate+ndeath);
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+                   int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-   if(estepm < stepm){
+ {  /* Some frequencies */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+   int i, m, jk, j1, bool, z1,j;
-   else  hstepm=estepm;
+   int mi; /* Effective wave */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   int first;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   double ***freq; /* Frequencies */
-      nhstepm is the number of hstepm from age to agelim
+   double *pp, **prop;
-      nstepm is the number of stepm from age to agelin.
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-      Look at hpijx to understand the reason of that which relies in memory size
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-      and note for a fixed period like k years */
+   double agebegin, ageend;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-      survival function given by stepm (the optimization length). Unfortunately it
+   pp=vector(1,nlstate);
-      means that if the survival funtion is printed every two years of age and if
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   strcpy(fileresp,"P_");
-      results. So we changed our mind and took the option of the best precision.
+   strcat(fileresp,fileresu);
-   */
+   /*strcat(fileresphtm,fileresu);*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-   agelim = AGESUP;
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     exit(0);
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   }
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
-     gp=matrix(0,nhstepm,1,nlstate);
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
-     gm=matrix(0,nhstepm,1,nlstate);
+     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fflush(ficlog);
-     for(theta=1; theta <=npar; theta++){
+     exit(70);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   else{
-       }
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+           fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-       if (popbased==1) {
+   }
-         if(mobilav ==0){
+     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);
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
-         }else{ /* mobilav */
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
-           for(i=1; i<=nlstate;i++)
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-         }
+     fflush(ficlog);
-       }
+     exit(70);
+   }
-       for(j=1; j<= nlstate; j++){
+   else{
-         for(h=0; h<=nhstepm; h++){
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
-         }
+           fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-       }
+   }
-       /* This for computing probability of death (h=1 means
+   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);
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-       */
+   j1=0;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+   j=cptcoveff;
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-       }
-       /* end probability of death */
+   first=1;
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+         scanf("%d", i);*/
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       for (i=-5; i<=nlstate+ndeath; i++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-       if (popbased==1) {
+           for(m=iagemin; m <= iagemax+3; m++)
-         if(mobilav ==0){
+             freq[i][jk][m]=0;
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+       for (i=1; i<=nlstate; i++)
-         }else{ /* mobilav */
+         for(m=iagemin; m <= iagemax+3; m++)
-           for(i=1; i<=nlstate;i++)
+           prop[i][m]=0;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+       dateintsum=0;
-       }
+       k2cpt=0;
+       for (i=1; i<=imx; i++) { /* For each individual i */
-       for(j=1; j<= nlstate; j++){
+         bool=1;
-         for(h=0; h<=nhstepm; h++){
+         if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+           for (z1=1; z1<=cptcoveff; z1++)
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-         }
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-       }
+               bool=0;
-       /* This for computing probability of death (h=1 means
+               /* 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",
-          computed over hstepm matrices product = hstepm*stepm months)
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-          as a weighted average of prlim.
+                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-       */
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+             }
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+         } /* cptcovn > 0 */
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+         if (bool==1){
-       /* end probability of death */
+           /* for(m=firstpass; m<=lastpass; m++){ */
+           for(mi=1; mi<wav[i];mi++){
-       for(j=1; j<= nlstate; j++) /* vareij */
+             m=mw[mi][i];
-         for(h=0; h<=nhstepm; h++){
+             /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+                and mw[mi+1][i]. dh depends on stepm. */
-         }
+             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+             ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+             if(m >=firstpass && m <=lastpass){
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+               k2=anint[m][i]+(mint[m][i]/12.);
-       }
+               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-     } /* End theta */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+               if (s[m][i]>0 && s[m][i]<=nlstate)  /* If status at wave m is known and a live state */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];  /* At age of beginning of transition, where status is known */
+               if (m<lastpass) {
-     for(h=0; h<=nhstepm; h++) /* veij */
+                 /* if(s[m][i]==4 && s[m+1][i]==4) */
-       for(j=1; j<=nlstate;j++)
+                 /*   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
-         for(theta=1; theta <=npar; theta++)
+                 if(s[m][i]==-1)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+                   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+                 /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
-       for(theta=1; theta <=npar; theta++)
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
-         trgradgp[j][theta]=gradgp[theta][j];
+               }
+             }
+             if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+               dateintsum=dateintsum+k2;
-     for(i=1;i<=nlstate;i++)
+               k2cpt++;
-       for(j=1;j<=nlstate;j++)
+               /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-         vareij[i][j][(int)age] =0.;
+             }
+             /*}*/
-     for(h=0;h<=nhstepm;h++){
+           } /* end m */
-       for(k=0;k<=nhstepm;k++){
+         } /* end bool */
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+       } /* end i = 1 to imx */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for(i=1;i<=nlstate;i++)
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-           for(j=1;j<=nlstate;j++)
+       pstamp(ficresp);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+       if  (cptcovn>0) {
-       }
+         fprintf(ficresp, "\n#********** Variable ");
-     }
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-     /* pptj */
+         for (z1=1; z1<=cptcoveff; z1++){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+           fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+           fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         }
-         varppt[j][i]=doldmp[j][i];
+           fprintf(ficresp, "**********\n#");
-     /* end ppptj */
+         fprintf(ficresphtm, "**********</h3>\n");
-     /*  x centered again */
+         fprintf(ficresphtmfr, "**********</h3>\n");
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+         fprintf(ficlog, "\n#********** Variable ");
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(ficlog, "**********\n");
-     if (popbased==1) {
+       }
-       if(mobilav ==0){
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-         for(i=1; i<=nlstate;i++)
+       for(i=1; i<=nlstate;i++) {
-           prlim[i][i]=probs[(int)age][i][ij];
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       }else{ /* mobilav */
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-         for(i=1; i<=nlstate;i++)
+       }
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+       fprintf(ficresp, "\n");
-       }
+       fprintf(ficresphtm, "\n");
-     }
+       /* Header of frequency table by age */
-     /* This for computing probability of death (h=1 means
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+       fprintf(ficresphtmfr,"<th>Age</th> ");
-        as a weighted average of prlim.
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
-     */
+         for(m=-1; m <=nlstate+ndeath; m++){
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+           if(jk!=0 && m!=0)
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         }
-     }
+       }
-     /* end probability of death */
+       fprintf(ficresphtmfr, "\n");
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+       /* For each age */
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       for(i=iagemin; i <= iagemax+3; i++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+         fprintf(ficresphtm,"<tr>");
-       for(i=1; i<=nlstate;i++){
+         if(i==iagemax+1){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+           fprintf(ficlog,"1");
-       }
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
-     }
+         }else if(i==iagemax+2){
-     fprintf(ficresprobmorprev,"\n");
+           fprintf(ficlog,"0");
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-     fprintf(ficresvij,"%.0f ",age );
+         }else if(i==iagemax+3){
-     for(i=1; i<=nlstate;i++)
+           fprintf(ficlog,"Total");
-       for(j=1; j<=nlstate;j++){
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+         }else{
-       }
+           if(first==1){
-     fprintf(ficresvij,"\n");
+             first=0;
-     free_matrix(gp,0,nhstepm,1,nlstate);
+             printf("See log file for details...\n");
-     free_matrix(gm,0,nhstepm,1,nlstate);
+           }
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+           fprintf(ficlog,"Age %d", i);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   } /* End age */
+         for(jk=1; jk <=nlstate ; jk++){
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+             pp[jk] += freq[jk][m][i];
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+         }
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+         for(jk=1; jk <=nlstate ; jk++){
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+           for(m=-1, pos=0; m <=0 ; m++)
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+             pos += freq[jk][m][i];
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+           if(pp[jk]>=1.e-10){
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+             if(first==1){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
- /*   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(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+           }else{
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+             if(first==1)
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+           }
- */
+         }
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-   free_vector(xp,1,npar);
+             pp[jk] += freq[jk][m][i];
-   free_matrix(doldm,1,nlstate,1,nlstate);
+         }
-   free_matrix(dnewm,1,nlstate,1,npar);
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+           pos += pp[jk];
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+           posprop += prop[jk][i];
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(jk=1; jk <=nlstate ; jk++){
-   fclose(ficresprobmorprev);
+           if(pos>=1.e-5){
-   fflush(ficgp);
+             if(first==1)
-   fflush(fichtm);
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- }  /* end varevsij */
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           }else{
- /************ Variance of prevlim ******************/
+             if(first==1)
- 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(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- {
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   /* Variance of prevalence limit */
+           }
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+           if( i <= iagemax){
-   double **newm;
+             if(pos>=1.e-5){
-   double **dnewm,**doldm;
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   int i, j, nhstepm, hstepm;
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   int k, cptcode;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   double *xp;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   double *gp, *gm;
+             }
-   double **gradg, **trgradg;
+             else{
-   double age,agelim;
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-   int theta;
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
+             }
-   pstamp(ficresvpl);
+           }
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+         }
-   fprintf(ficresvpl,"# Age");
-   for(i=1; i<=nlstate;i++)
+         for(jk=-1; jk <=nlstate+ndeath; jk++){
-       fprintf(ficresvpl," %1d-%1d",i,i);
+           for(m=-1; m <=nlstate+ndeath; m++){
-   fprintf(ficresvpl,"\n");
+             if(freq[jk][m][i] !=0 ) { /* minimizing output */
+               if(first==1){
-   xp=vector(1,npar);
+                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   dnewm=matrix(1,nlstate,1,npar);
+               }
-   doldm=matrix(1,nlstate,1,nlstate);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
-   hstepm=1*YEARM; /* Every year of age */
+             if(jk!=0 && m!=0)
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
-   agelim = AGESUP;
+           }
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+         }
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         fprintf(ficresphtmfr,"</tr>\n ");
-     if (stepm >= YEARM) hstepm=1;
+         if(i <= iagemax){
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           fprintf(ficresp,"\n");
-     gradg=matrix(1,npar,1,nlstate);
+           fprintf(ficresphtm,"</tr>\n");
-     gp=vector(1,nlstate);
+         }
-     gm=vector(1,nlstate);
+         if(first==1)
+           printf("Others in log...\n");
-     for(theta=1; theta <=npar; theta++){
+         fprintf(ficlog,"\n");
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+       } /* end loop i */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       fprintf(ficresphtm,"</table>\n");
-       }
+       fprintf(ficresphtmfr,"</table>\n");
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       /*}*/
-       for(i=1;i<=nlstate;i++)
+   } /* end j1 */
-         gp[i] = prlim[i][i];
+   dateintmean=dateintsum/k2cpt;
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   fclose(ficresp);
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   fclose(ficresphtm);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   fclose(ficresphtmfr);
-       for(i=1;i<=nlstate;i++)
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-         gm[i] = prlim[i][i];
+   free_vector(pp,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-       for(i=1;i<=nlstate;i++)
+   /* End of Freq */
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+ }
-     } /* End theta */
+ /************ Prevalence ********************/
-     trgradg =matrix(1,nlstate,1,npar);
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ {
-     for(j=1; j<=nlstate;j++)
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-       for(theta=1; theta <=npar; theta++)
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-         trgradg[j][theta]=gradg[theta][j];
+      We still use firstpass and lastpass as another selection.
+   */
-     for(i=1;i<=nlstate;i++)
-       varpl[i][(int)age] =0.;
+   int i, m, jk, j1, bool, z1,j;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   int mi; /* Effective wave */
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   int iage;
-     for(i=1;i<=nlstate;i++)
+   double agebegin, ageend;
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   double **prop;
-     fprintf(ficresvpl,"%.0f ",age );
+   double posprop;
-     for(i=1; i<=nlstate;i++)
+   double  y2; /* in fractional years */
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   int iagemin, iagemax;
-     fprintf(ficresvpl,"\n");
+   int first; /** to stop verbosity which is redirected to log file */
-     free_vector(gp,1,nlstate);
-     free_vector(gm,1,nlstate);
+   iagemin= (int) agemin;
-     free_matrix(gradg,1,npar,1,nlstate);
+   iagemax= (int) agemax;
-     free_matrix(trgradg,1,nlstate,1,npar);
+   /*pp=vector(1,nlstate);*/
-   } /* End age */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   free_vector(xp,1,npar);
+   j1=0;
-   free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   /*j=cptcoveff;*/
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
- }
+   first=1;
- /************ Variance of one-step probabilities  ******************/
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+     for (i=1; i<=nlstate; i++)
- {
+       for(iage=iagemin; iage <= iagemax+3; iage++)
-   int i, j=0,  i1, k1, l1, t, tj;
+         prop[i][iage]=0.0;
-   int k2, l2, j1,  z1;
-   int k=0,l, cptcode;
+     for (i=1; i<=imx; i++) { /* Each individual */
-   int first=1, first1;
+       bool=1;
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-   double **dnewm,**doldm;
+         for (z1=1; z1<=cptcoveff; z1++)
-   double *xp;
+           if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
-   double *gp, *gm;
+             bool=0;
-   double **gradg, **trgradg;
+       }
-   double **mu;
+       if (bool==1) {
-   double age,agelim, cov[NCOVMAX];
+         /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+         for(mi=1; mi<wav[i];mi++){
-   int theta;
+           m=mw[mi][i];
-   char fileresprob[FILENAMELENGTH];
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-   char fileresprobcov[FILENAMELENGTH];
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-   char fileresprobcor[FILENAMELENGTH];
+           if(m >=firstpass && m <=lastpass){
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   double ***varpij;
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-   strcpy(fileresprob,"prob");
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-   strcat(fileresprob,fileres);
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-     printf("Problem with resultfile: %s\n", fileresprob);
+                 /*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]]);*/
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
-   }
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   strcpy(fileresprobcov,"probcov");
+               } /* end valid statuses */
-   strcat(fileresprobcov,fileres);
+             } /* end selection of dates */
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+           } /* end selection of waves */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+         } /* end effective waves */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+       } /* end bool */
-   }
+     }
-   strcpy(fileresprobcor,"probcor");
+     for(i=iagemin; i <= iagemax+3; i++){
-   strcat(fileresprobcor,fileres);
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+         posprop += prop[jk][i];
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+       }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+       for(jk=1; jk <=nlstate ; jk++){
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+         if( i <=  iagemax){
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+           if(posprop>=1.e-5){
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+           } else{
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+             if(first==1){
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+               first=0;
-   pstamp(ficresprob);
+               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]);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+             }
-   fprintf(ficresprob,"# Age");
+           }
-   pstamp(ficresprobcov);
+         }
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+       }/* end jk */
-   fprintf(ficresprobcov,"# Age");
+     }/* end i */
-   pstamp(ficresprobcor);
+     /*} *//* end i1 */
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   } /* end j1 */
-   fprintf(ficresprobcor,"# Age");
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*free_vector(pp,1,nlstate);*/
-   for(i=1; i<=nlstate;i++)
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-     for(j=1; j<=(nlstate+ndeath);j++){
+ }  /* End of prevalence */
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+ /************* Waves Concatenation ***************/
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+ 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)
-  /* fprintf(ficresprob,"\n");
+ {
-   fprintf(ficresprobcov,"\n");
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   fprintf(ficresprobcor,"\n");
+      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
-  xp=vector(1,npar);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      and mw[mi+1][i]. dh depends on stepm.
-   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);
+   int i, mi, m;
-   first=1;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   fprintf(ficgp,"\n# Routine varprob");
+      double sum=0., jmean=0.;*/
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   int first, firstwo;
-   fprintf(fichtm,"\n");
+   int j, k=0,jk, ju, jl;
+   double sum=0.;
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   first=0;
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   firstwo=0;
-   file %s<br>\n",optionfilehtmcov);
+   jmin=100000;
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   jmax=-1;
- and drawn. It helps understanding how is the covariance between two incidences.\
+   jmean=0.;
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
-   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. \
+     mi=0;
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+     m=firstpass;
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+     while(s[m][i] <= nlstate){  /* a live state */
- standard deviations wide on each axis. <br>\
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+         mw[++mi][i]=m;
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+       if(m >=lastpass)
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+         break;
+       else
-   cov[1]=1;
+         m++;
-   tj=cptcoveff;
+     }/* end while */
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     if (s[m][i] > nlstate){  /* In a death state */
-   j1=0;
+       mi++;     /* Death is another wave */
-   for(t=1; t<=tj;t++){
+       /* if(mi==0)  never been interviewed correctly before death */
-     for(i1=1; i1<=ncodemax[t];i1++){
+          /* Only death is a correct wave */
-       j1++;
+       mw[mi][i]=m;
-       if  (cptcovn>0) {
+     }else if (andc[i] != 9999) { /* A death occured after lastpass */
-         fprintf(ficresprob, "\n#********** Variable ");
+       m++;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       mi++;
-         fprintf(ficresprob, "**********\n#\n");
+       s[m][i]=nlstate+1;  /* We are setting the status to the last of non live state */
-         fprintf(ficresprobcov, "\n#********** Variable ");
+       mw[mi][i]=m;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       nbwarn++;
-         fprintf(ficresprobcov, "**********\n#\n");
+       if(firstwo==0){
+         printf("Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
-         fprintf(ficgp, "\n#********** Variable ");
+         fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         firstwo=1;
-         fprintf(ficgp, "**********\n#\n");
+       }
+       if(firstwo==1){
+         fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+       }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     }
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+     wav[i]=mi;
+     if(mi==0){
-         fprintf(ficresprobcor, "\n#********** Variable ");
+       nbwarn++;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       if(first==0){
-         fprintf(ficresprobcor, "**********\n#");
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-       }
+         first=1;
+       }
-       for (age=bage; age<=fage; age ++){
+       if(first==1){
-         cov[2]=age;
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-         for (k=1; k<=cptcovn;k++) {
+       }
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+     } /* end mi==0 */
-         }
+   } /* End individuals */
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   /* wav and mw are no more changed */
-         for (k=1; k<=cptcovprod;k++)
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   for(i=1; i<=imx; i++){
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+     for(mi=1; mi<wav[i];mi++){
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       if (stepm <=0)
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         dh[mi][i]=1;
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+       else{
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-         for(theta=1; theta <=npar; theta++){
+           if (agedc[i] < 2*AGESUP) {
-           for(i=1; i<=npar; i++)
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+             if(j==0) j=1;  /* Survives at least one month after exam */
+             else if(j<0){
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+               nberr++;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           k=0;
+               j=1; /* Temporary Dangerous patch */
-           for(i=1; i<= (nlstate); i++){
+               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);
-             for(j=1; j<=(nlstate+ndeath);j++){
+               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]);
-               k=k+1;
+               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);
-               gp[k]=pmmij[i][j];
+             }
-             }
+             k=k+1;
-           }
+             if (j >= jmax){
+               jmax=j;
-           for(i=1; i<=npar; i++)
+               ijmax=i;
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+             }
+             if (j <= jmin){
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+               jmin=j;
-           k=0;
+               ijmin=i;
-           for(i=1; i<=(nlstate); i++){
+             }
-             for(j=1; j<=(nlstate+ndeath);j++){
+             sum=sum+j;
-               k=k+1;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-               gm[k]=pmmij[i][j];
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-             }
+           }
-           }
+         }
+         else{
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-         }
+           k=k+1;
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+           if (j >= jmax) {
-           for(theta=1; theta <=npar; theta++)
+             jmax=j;
-             trgradg[j][theta]=gradg[theta][j];
+             ijmax=i;
+           }
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+           else if (j <= jmin){
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+             jmin=j;
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+             ijmin=i;
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+           }
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+           /*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){
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+             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]);
-         k=0;
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         for(i=1; i<=(nlstate); i++){
+           }
-           for(j=1; j<=(nlstate+ndeath);j++){
+           sum=sum+j;
-             k=k+1;
+         }
-             mu[k][(int) age]=pmmij[i][j];
+         jk= j/stepm;
-           }
+         jl= j -jk*stepm;
-         }
+         ju= j -(jk+1)*stepm;
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+           if(jl==0){
-             varpij[i][j][(int)age] = doldm[i][j];
+             dh[mi][i]=jk;
+             bh[mi][i]=0;
-         /*printf("\n%d ",(int)age);
+           }else{ /* We want a negative bias in order to only have interpolation ie
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+                   * to avoid the price of an extra matrix product in likelihood */
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+             dh[mi][i]=jk+1;
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+             bh[mi][i]=ju;
-           }*/
+           }
+         }else{
-         fprintf(ficresprob,"\n%d ",(int)age);
+           if(jl <= -ju){
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+             dh[mi][i]=jk;
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+             bh[mi][i]=jl;       /* bias is positive if real duration
+                                  * is higher than the multiple of stepm and negative otherwise.
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+                                  */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+           }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           else{
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+             dh[mi][i]=jk+1;
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+             bh[mi][i]=ju;
-         }
+           }
-         i=0;
+           if(dh[mi][i]==0){
-         for (k=1; k<=(nlstate);k++){
+             dh[mi][i]=1; /* At least one step */
-           for (l=1; l<=(nlstate+ndeath);l++){
+             bh[mi][i]=ju; /* At least one step */
-             i=i++;
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+           }
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+         } /* end if mle */
-             for (j=1; j<=i;j++){
+       }
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+     } /* end wave */
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+   }
-             }
+   jmean=sum/k;
-           }
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-         }/* end of loop for state */
+   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);
-       } /* end of loop for age */
+  }
-       /* Confidence intervalle of pij  */
+ /*********** Tricode ****************************/
-       /*
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-         fprintf(ficgp,"\nset noparametric;unset label");
+ {
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-         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);
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+    * nbcode[Tvar[j]][1]=
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+   */
-       */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+   int modmaxcovj=0; /* Modality max of covariates j */
-       first1=1;
+   int cptcode=0; /* Modality max of covariates j */
-       for (k2=1; k2<=(nlstate);k2++){
+   int modmincovj=0; /* Modality min of covariates j */
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
+   cptcoveff=0;
-           for (k1=1; k1<=(nlstate);k1++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+   /* Loop on covariates without age and products */
-               if(i<=j) continue;
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
-               for (age=bage; age<=fage; age ++){
+     for (k=-1; k < maxncov; k++) Ndum[k]=0;
-                 if ((int)age %5==0){
+     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                                modality of this covariate Vj*/
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                                     * If product of Vn*Vm, still boolean *:
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-                   c12=cv12/sqrt(v1*v2);
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                   /* Computing eigen value of matrix of covariance */
+                                       modality of the nth covariate of individual i. */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       if (ij > modmaxcovj)
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+         modmaxcovj=ij;
-                   /* Eigen vectors */
+       else if (ij < modmincovj)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+         modmincovj=ij;
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+       if ((ij < -1) && (ij > NCOVMAX)){
-                   v21=(lc1-v1)/cv12*v11;
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-                   v12=-v21;
+         exit(1);
-                   v22=v11;
+       }else
-                   tnalp=v21/v11;
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-                   if(first1==1){
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-                     first1=0;
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-                     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);
+       /* getting the maximum value of the modality of the covariate
-                   }
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                   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);
+          female is 1, then modmaxcovj=1.*/
-                   /*printf(fignu*/
+     } /* end for loop on individuals i */
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-                   if(first==1){
+     cptcode=modmaxcovj;
-                     first=0;
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                     fprintf(ficgp,"\nset parametric;unset label");
+    /*for (i=0; i<=cptcode; i++) {*/
-                     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);
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+         if( k != -1){
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                              covariate for which somebody answered excluding
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                              undefined. Usually 2: 0 and 1. */
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+         }
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                              covariate for which somebody answered including
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                              undefined. Usually 3: -1, 0 and 1. */
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+       }
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-                   }else{
+     } /* Ndum[-1] number of undefined modalities */
-                     first=0;
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
-                     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",\
+        modmincovj=3; modmaxcovj = 7;
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-                   }/* if first */
+        defining two dummy variables: variables V1_1 and V1_2.
-                 } /* age mod 5 */
+        nbcode[Tvar[j]][ij]=k;
-               } /* end loop age */
+        nbcode[Tvar[j]][1]=0;
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+        nbcode[Tvar[j]][2]=1;
-               first=1;
+        nbcode[Tvar[j]][3]=2;
-             } /*l12 */
+        To be continued (not working yet).
-           } /* k12 */
+     */
-         } /*l1 */
+     ij=0; /* ij is similar to i but can jump over null modalities */
-       }/* k1 */
+     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*/
-     } /* loop covariates */
+         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-   }
+           break;
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+         }
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+         ij++;
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+         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.*/
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+         cptcode = ij; /* New max modality for covar j */
-   free_vector(xp,1,npar);
+     } /* end of loop on modality i=-1 to 1 or more */
-   fclose(ficresprob);
-   fclose(ficresprobcov);
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-   fclose(ficresprobcor);
+     /*  /\*recode from 0 *\/ */
-   fflush(ficgp);
+     /*                               k is a modality. If we have model=V1+V1*sex  */
-   fflush(fichtmcov);
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
- }
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+     /*  } */
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
- /******************* Printing html file ***********/
+     /*  if (ij > ncodemax[j]) { */
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-                   int lastpass, int stepm, int weightopt, char model[],\
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     /*    break; */
-                   int popforecast, int estepm ,\
+     /*  } */
-                   double jprev1, double mprev1,double anprev1, \
+     /*   }  /\* end of loop on modality k *\/ */
-                   double jprev2, double mprev2,double anprev2){
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   int jj1, k1, i1, cpt;
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-    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 \
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
- </ul>");
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+    Ndum[ij]++; /* Might be supersed V1 + V1*age */
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+  }
-    fprintf(fichtm,"\
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+  ij=0;
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-    fprintf(fichtm,"\
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+      ij++;
-    fprintf(fichtm,"\
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-  - (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): \
+      Tvaraff[ij]=i; /*For printing (unclear) */
-    <a href=\"%s\">%s</a> <br>\n",
+    }else{
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+        /* Tvaraff[ij]=0; */
-    fprintf(fichtm,"\
+    }
-  - Population projections by age and states: \
+  }
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+  /* ij--; */
+  cptcoveff=ij; /*Number of total covariates*/
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+ }
-  m=cptcoveff;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ /*********** Health Expectancies ****************/
-  jj1=0;
-  for(k1=1; k1<=m;k1++){
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      jj1++;
+ {
-      if (cptcovn > 0) {
+   /* Health expectancies, no variances */
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   int i, j, nhstepm, hstepm, h, nstepm;
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   int nhstepma, nstepma; /* Decreasing with age */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   double age, agelim, hf;
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   double ***p3mat;
-      }
+   double eip;
-      /* 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> \
+   pstamp(ficreseij);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-      /* Quasi-incidences */
+   fprintf(ficreseij,"# Age");
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+   for(i=1; i<=nlstate;i++){
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+     for(j=1; j<=nlstate;j++){
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       fprintf(ficreseij," e%1d%1d ",i,j);
-        /* Period (stable) prevalence in each health state */
+     }
-        for(cpt=1; cpt<nlstate;cpt++){
+     fprintf(ficreseij," e%1d. ",i);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+   }
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+   fprintf(ficreseij,"\n");
-        }
-      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+   if(estepm < stepm){
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-      }
+   }
-    } /* end i1 */
+   else  hstepm=estepm;
-  }/* End k1 */
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-  fprintf(fichtm,"</ul>");
+    * 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
-  fprintf(fichtm,"\
+    * progression in between and thus overestimating or underestimating according
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+    * to the curvature of the survival function. If, for the same date, we
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+    * 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
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+    * hypothesis. A more precise result, taking into account a more precise
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+    * curvature will be obtained if estepm is as small as stepm. */
-  fprintf(fichtm,"\
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   /* For example we decided to compute the life expectancy with the smallest unit */
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
-  fprintf(fichtm,"\
+      nstepm is the number of stepm from age to agelin.
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+      Look at hpijx to understand the reason of that which relies in memory size
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+      and note for a fixed period like estepm months */
-  fprintf(fichtm,"\
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-  - 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): \
+      survival function given by stepm (the optimization length). Unfortunately it
-    <a href=\"%s\">%s</a> <br>\n</li>",
+      means that if the survival funtion is printed only each two years of age and if
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-  fprintf(fichtm,"\
+      results. So we changed our mind and took the option of the best precision.
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+   */
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-  fprintf(fichtm,"\
+   agelim=AGESUP;
-  - 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",
+   /* If stepm=6 months */
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-  fprintf(fichtm,"\
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-  - 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",
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ /* nhstepm age range expressed in number of stepm */
-  fprintf(fichtm,"\
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*  - 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 */
+   for (age=bage; age<=fage; age ++){
- /*      <br>",fileres,fileres,fileres,fileres); */
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /*  else  */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /*    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 (stepm >= YEARM) hstepm=1;*/
-  fflush(fichtm);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+     /* If stepm=6 months */
-  m=cptcoveff;
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-  jj1=0;
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-      jj1++;
-      if (cptcovn > 0) {
+     printf("%d|",(int)age);fflush(stdout);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     /* Computing expectancies */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     for(i=1; i<=nlstate;i++)
-      }
+       for(j=1; j<=nlstate;j++)
-      for(cpt=1; cpt<=nlstate;cpt++) {
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+           /* 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]);*/
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+         }
- health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+     fprintf(ficreseij,"%3.0f",age );
-    } /* end i1 */
+     for(i=1; i<=nlstate;i++){
-  }/* End k1 */
+       eip=0;
-  fprintf(fichtm,"</ul>");
+       for(j=1; j<=nlstate;j++){
-  fflush(fichtm);
+         eip +=eij[i][j][(int)age];
- }
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
- /******************* Gnuplot file **************/
+       fprintf(ficreseij,"%9.4f", eip );
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     }
+     fprintf(ficreseij,"\n");
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   }
-   int ng;
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+   printf("\n");
- /*     printf("Problem with file %s",optionfilegnuplot); */
+   fprintf(ficlog,"\n");
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- /*   } */
+ }
-   /*#ifdef windows */
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+ {
-   m=pow(2,cptcoveff);
+   /* Covariances of health expectancies eij and of total life expectancies according
+    to initial status i, ei. .
-   strcpy(dirfileres,optionfilefiname);
+   */
-   strcpy(optfileres,"vpl");
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-  /* 1eme*/
+   int nhstepma, nstepma; /* Decreasing with age */
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   double age, agelim, hf;
-    for (k1=1; k1<= m ; k1 ++) {
+   double ***p3matp, ***p3matm, ***varhe;
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   double **dnewm,**doldm;
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+   double *xp, *xm;
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+   double **gp, **gm;
- set ylabel \"Probability\" \n\
+   double ***gradg, ***trgradg;
- set ter png small\n\
+   int theta;
- set size 0.65,0.65\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+   double eip, vip;
-      for (i=1; i<= nlstate ; i ++) {
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   xp=vector(1,npar);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   xm=vector(1,npar);
-      }
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-      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);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-      for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   pstamp(ficresstdeij);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-      }
+   fprintf(ficresstdeij,"# Age");
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+   for(i=1; i<=nlstate;i++){
-      for (i=1; i<= nlstate ; i ++) {
+     for(j=1; j<=nlstate;j++)
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+     fprintf(ficresstdeij," e%1d. ",i);
-      }
+   }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+   fprintf(ficresstdeij,"\n");
-    }
-   }
+   pstamp(ficrescveij);
-   /*2 eme*/
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
-   for (k1=1; k1<= m ; k1 ++) {
+   for(i=1; i<=nlstate;i++)
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+     for(j=1; j<=nlstate;j++){
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
-     for (i=1; i<= nlstate+1 ; i ++) {
+         for(j2=1; j2<=nlstate;j2++){
-       k=2*i;
+           cptj2= (j2-1)*nlstate+i2;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+           if(cptj2 <= cptj)
-       for (j=1; j<= nlstate+1 ; j ++) {
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         }
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+     }
-       }
+   fprintf(ficrescveij,"\n");
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+   if(estepm < stepm){
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       for (j=1; j<= nlstate+1 ; j ++) {
+   }
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else  hstepm=estepm;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-       }
+    * This is mainly to measure the difference between two models: for example
-       fprintf(ficgp,"\" t\"\" w l 0,");
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-       for (j=1; j<= nlstate+1 ; j ++) {
+    * progression in between and thus overestimating or underestimating according
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+    * to the curvature of the survival function. If, for the same date, we
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+    * 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
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+    * hypothesis. A more precise result, taking into account a more precise
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+    * curvature will be obtained if estepm is as small as stepm. */
-     }
-   }
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   /*3eme*/
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
-   for (k1=1; k1<= m ; k1 ++) {
+      Look at hpijx to understand the reason of that which relies in memory size
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+      and note for a fixed period like estepm months */
-       /*       k=2+nlstate*(2*cpt-2); */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       k=2+(nlstate+1)*(cpt-1);
+      survival function given by stepm (the optimization length). Unfortunately it
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+      means that if the survival funtion is printed only each two years of age and if
-       fprintf(ficgp,"set ter png small\n\
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
- set size 0.65,0.65\n\
+      results. So we changed our mind and took the option of the best precision.
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+   */
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   /* If stepm=6 months */
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+   /* nhstepm age range expressed in number of stepm */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+   agelim=AGESUP;
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       */
+   /* if (stepm >= YEARM) hstepm=1;*/
-       for (i=1; i< nlstate ; i ++) {
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     }
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   }
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   /* CV preval stable (period) */
+   for (age=bage; age<=fage; age ++){
-   for (k1=1; k1<= m ; k1 ++) {
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       k=3;
+     /* if (stepm >= YEARM) hstepm=1;*/
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter png small\nset size 0.65,0.65\n\
+     /* If stepm=6 months */
- unset log y\n\
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       for (i=1; i< nlstate ; i ++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         fprintf(ficgp,"+$%d",k+i+1);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-       l=3+(nlstate+ndeath)*cpt;
+        decrease memory allocation */
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+     for(theta=1; theta <=npar; theta++){
-       for (i=1; i< nlstate ; i ++) {
+       for(i=1; i<=npar; i++){
-         l=3+(nlstate+ndeath)*cpt;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         fprintf(ficgp,"+$%d",l+i+1);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-     }
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   }
+       for(j=1; j<= nlstate; j++){
-   /* proba elementaires */
+         for(i=1; i<=nlstate; i++){
-   for(i=1,jk=1; i <=nlstate; i++){
+           for(h=0; h<=nhstepm-1; h++){
-     for(k=1; k <=(nlstate+ndeath); k++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-       if (k != i) {
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-         for(j=1; j <=ncovmodel; j++){
+           }
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+         }
-           jk++;
+       }
-           fprintf(ficgp,"\n");
-         }
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-       }
+         for(h=0; h<=nhstepm-1; h++){
-     }
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-    }
+         }
+     }/* End theta */
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-      for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+     for(h=0; h<=nhstepm-1; h++)
-        if (ng==2)
+       for(j=1; j<=nlstate*nlstate;j++)
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+         for(theta=1; theta <=npar; theta++)
-        else
+           trgradg[h][j][theta]=gradg[h][theta][j];
-          fprintf(ficgp,"\nset title \"Probability\"\n");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-        i=1;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-        for(k2=1; k2<=nlstate; k2++) {
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-          k3=i;
+         varhe[ij][ji][(int)age] =0.;
-          for(k=1; k<=(nlstate+ndeath); k++) {
-            if (k != k2){
+      printf("%d|",(int)age);fflush(stdout);
-              if(ng==2)
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+      for(h=0;h<=nhstepm-1;h++){
-              else
+       for(k=0;k<=nhstepm-1;k++){
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-              ij=1;
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-              for(j=3; j <=ncovmodel; j++) {
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-                  ij++;
+       }
-                }
+     }
-                else
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     /* Computing expectancies */
-              }
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-              fprintf(ficgp,")/(1");
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
-              for(k1=1; k1 <=nlstate; k1++){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-                ij=1;
-                for(j=3; j <=ncovmodel; j++){
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-                  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]]]);
+         }
-                    ij++;
-                  }
+     fprintf(ficresstdeij,"%3.0f",age );
-                  else
+     for(i=1; i<=nlstate;i++){
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       eip=0.;
-                }
+       vip=0.;
-                fprintf(ficgp,")");
+       for(j=1; j<=nlstate;j++){
-              }
+         eip += eij[i][j][(int)age];
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-              i=i+ncovmodel;
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-            }
+       }
-          } /* end k */
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-        } /* end k2 */
+     }
-      } /* end jk */
+     fprintf(ficresstdeij,"\n");
-    } /* end ng */
-    fflush(ficgp);
+     fprintf(ficrescveij,"%3.0f",age );
- }  /* end gnuplot */
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
+         cptj= (j-1)*nlstate+i;
- /*************** Moving average **************/
+         for(i2=1; i2<=nlstate;i2++)
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
-   int i, cpt, cptcod;
+             if(cptj2 <= cptj)
-   int modcovmax =1;
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-   int mobilavrange, mob;
+           }
-   double age;
+       }
+     fprintf(ficrescveij,"\n");
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-                            a covariate has 2 modalities */
+   }
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     if(mobilav==1) mobilavrange=5; /* default */
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     else mobilavrange=mobilav;
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for (age=bage; age<=fage; age++)
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for (i=1; i<=nlstate;i++)
+   printf("\n");
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+   fprintf(ficlog,"\n");
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-     /* We keep the original values on the extreme ages bage, fage and for
+   free_vector(xm,1,npar);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+   free_vector(xp,1,npar);
-        we use a 5 terms etc. until the borders are no more concerned.
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-     */
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+ }
-         for (i=1; i<=nlstate;i++){
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+ /************ Variance ******************/
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+  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[])
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+ {
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+   /* Variance of health expectancies */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-               }
+   /* double **newm;*/
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-           }
-         }
+   int movingaverage();
-       }/* end age */
+   double **dnewm,**doldm;
-     }/* end mob */
+   double **dnewmp,**doldmp;
-   }else return -1;
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   return 0;
+   int k;
- }/* End movingaverage */
+   double *xp;
+   double **gp, **gm;  /* for var eij */
+   double ***gradg, ***trgradg; /*for var eij */
- /************** Forecasting ******************/
+   double **gradgp, **trgradgp; /* for var p point j */
- 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){
+   double *gpp, *gmp; /* for var p point j */
-   /* proj1, year, month, day of starting projection
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-      agemin, agemax range of age
+   double ***p3mat;
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+   double age,agelim, hf;
-      anproj2 year of en of projection (same day and month as proj1).
+   double ***mobaverage;
-   */
+   int theta;
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+   char digit[4];
-   int *popage;
+   char digitp[25];
-   double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   char fileresprobmorprev[FILENAMELENGTH];
-   double *popeffectif,*popcount;
-   double ***p3mat;
+   if(popbased==1){
-   double ***mobaverage;
+     if(mobilav!=0)
-   char fileresf[FILENAMELENGTH];
+       strcpy(digitp,"-POPULBASED-MOBILAV_");
+     else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-   agelim=AGESUP;
+   }
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   else
+     strcpy(digitp,"-STABLBASED_");
-   strcpy(fileresf,"f");
-   strcat(fileresf,fileres);
+   if (mobilav!=0) {
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   }
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+     }
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   }
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   strcpy(fileresprobmorprev,"PRMORPREV-");
+   sprintf(digit,"%-d",ij);
-   if (mobilav!=0) {
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   strcat(fileresprobmorprev,fileresu);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     }
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   if (stepm<=12) stepsize=1;
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   if(estepm < stepm){
+   pstamp(ficresprobmorprev);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   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);
-   else  hstepm=estepm;
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   hstepm=hstepm/stepm;
+     for(i=1; i<=nlstate;i++)
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-                                fractional in yp1 */
+   }
-   anprojmean=yp;
+   fprintf(ficresprobmorprev,"\n");
-   yp2=modf((yp1*12),&yp);
-   mprojmean=yp;
+   fprintf(ficgp,"\n# Routine varevsij");
-   yp1=modf((yp2*30.5),&yp);
+   fprintf(ficgp,"\nunset title \n");
-   jprojmean=yp;
+ /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   if(jprojmean==0) jprojmean=1;
+   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");
-   if(mprojmean==0) jprojmean=1;
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ /*   } */
-   i1=cptcoveff;
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (cptcovn < 1){i1=1;}
+   pstamp(ficresvij);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   else
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
- /*            if (h==(int)(YEARM*yearp)){ */
+   fprintf(ficresvij,"# Age");
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   for(i=1; i<=nlstate;i++)
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     for(j=1; j<=nlstate;j++)
-       k=k+1;
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-       fprintf(ficresf,"\n#******");
+   fprintf(ficresvij,"\n");
-       for(j=1;j<=cptcoveff;j++) {
-         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]]);
+   xp=vector(1,npar);
-       }
+   dnewm=matrix(1,nlstate,1,npar);
-       fprintf(ficresf,"******\n");
+   doldm=matrix(1,nlstate,1,nlstate);
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-       for(j=1; j<=nlstate+ndeath;j++){
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         for(i=1; i<=nlstate;i++)
-           fprintf(ficresf," p%d%d",i,j);
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-         fprintf(ficresf," p.%d",j);
+   gpp=vector(nlstate+1,nlstate+ndeath);
-       }
+   gmp=vector(nlstate+1,nlstate+ndeath);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-         fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+   }
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+   else  hstepm=estepm;
-           nhstepm = nhstepm/hstepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-           oldm=oldms;savm=savms;
+      nhstepm is the number of hstepm from age to agelim
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+      nstepm is the number of stepm from age to agelim.
+      Look at function hpijx to understand why because of memory size limitations,
-           for (h=0; h<=nhstepm; h++){
+      we decided (b) to get a life expectancy respecting the most precise curvature of the
-             if (h*hstepm/YEARM*stepm ==yearp) {
+      survival function given by stepm (the optimization length). Unfortunately it
-               fprintf(ficresf,"\n");
+      means that if the survival funtion is printed every two years of age and if
-               for(j=1;j<=cptcoveff;j++)
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      results. So we changed our mind and took the option of the best precision.
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+   */
-             }
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-             for(j=1; j<=nlstate+ndeath;j++) {
+   agelim = AGESUP;
-               ppij=0.;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-               for(i=1; i<=nlstate;i++) {
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-                 if (mobilav==1)
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                 else {
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+     gp=matrix(0,nhstepm,1,nlstate);
-                 }
+     gm=matrix(0,nhstepm,1,nlstate);
-                 if (h*hstepm/YEARM*stepm== yearp) {
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
+     for(theta=1; theta <=npar; theta++){
-               } /* end i */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-               if (h*hstepm/YEARM*stepm==yearp) {
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-                 fprintf(ficresf," %.3f", ppij);
+       }
-               }
-             }/* end j */
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-           } /* end h */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       if (popbased==1) {
-         } /* end agec */
+         if(mobilav ==0){
-       } /* end yearp */
+           for(i=1; i<=nlstate;i++)
-     } /* end cptcod */
+             prlim[i][i]=probs[(int)age][i][ij];
-   } /* end  cptcov */
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-   fclose(ficresf);
+       }
- }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
- /************** Forecasting *****not tested NB*************/
+       for(j=1; j<= nlstate; j++){
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+         for(h=0; h<=nhstepm; h++){
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-   int *popage;
+         }
-   double calagedatem, agelim, kk1, kk2;
+       }
-   double *popeffectif,*popcount;
+       /* Next for computing probability of death (h=1 means
-   double ***p3mat,***tabpop,***tabpopprev;
+          computed over hstepm matrices product = hstepm*stepm months)
-   double ***mobaverage;
+          as a weighted average of prlim.
-   char filerespop[FILENAMELENGTH];
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-   agelim=AGESUP;
+       }
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+       /* end probability of death */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   strcpy(filerespop,"pop");
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
-   strcat(filerespop,fileres);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+       if (popbased==1) {
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+         if(mobilav ==0){
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+           for(i=1; i<=nlstate;i++)
-   }
+             prlim[i][i]=probs[(int)age][i][ij];
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+         }else{ /* mobilav */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+         }
+       }
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         for(h=0; h<=nhstepm; h++){
-     }
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-   }
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+         }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+       }
-   if (stepm<=12) stepsize=1;
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-   agelim=AGESUP;
+          as a weighted average of prlim.
+       */
-   hstepm=1;
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   hstepm=hstepm/stepm;
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-   if (popforecast==1) {
+       }
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+       /* end probability of death */
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+       for(j=1; j<= nlstate; j++) /* vareij */
-     }
+         for(h=0; h<=nhstepm; h++){
-     popage=ivector(0,AGESUP);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-     popeffectif=vector(0,AGESUP);
+         }
-     popcount=vector(0,AGESUP);
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-     i=1;
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+       }
-     imx=i;
+     } /* End theta */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+     for(h=0; h<=nhstepm; h++) /* veij */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       for(j=1; j<=nlstate;j++)
-       k=k+1;
+         for(theta=1; theta <=npar; theta++)
-       fprintf(ficrespop,"\n#******");
+           trgradg[h][j][theta]=gradg[h][theta][j];
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       }
+       for(theta=1; theta <=npar; theta++)
-       fprintf(ficrespop,"******\n");
+         trgradgp[j][theta]=gradgp[theta][j];
-       fprintf(ficrespop,"# Age");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     for(i=1;i<=nlstate;i++)
-       for (cpt=0; cpt<=0;cpt++) {
+       for(j=1;j<=nlstate;j++)
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         vareij[i][j][(int)age] =0.;
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     for(h=0;h<=nhstepm;h++){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       for(k=0;k<=nhstepm;k++){
-           nhstepm = nhstepm/hstepm;
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(i=1;i<=nlstate;i++)
-           oldm=oldms;savm=savms;
+           for(j=1;j<=nlstate;j++)
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+       }
-           for (h=0; h<=nhstepm; h++){
+     }
-             if (h==(int) (calagedatem+YEARM*cpt)) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+     /* pptj */
-             }
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-             for(j=1; j<=nlstate+ndeath;j++) {
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-               kk1=0.;kk2=0;
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-               for(i=1; i<=nlstate;i++) {
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-                 if (mobilav==1)
+         varppt[j][i]=doldmp[j][i];
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+     /* end ppptj */
-                 else {
+     /*  x centered again */
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 }
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
-               }
-               if (h==(int)(calagedatem+12*cpt)){
+     if (popbased==1) {
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+       if(mobilav ==0){
-                   /*fprintf(ficrespop," %.3f", kk1);
+         for(i=1; i<=nlstate;i++)
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+           prlim[i][i]=probs[(int)age][i][ij];
-               }
+       }else{ /* mobilav */
-             }
+         for(i=1; i<=nlstate;i++)
-             for(i=1; i<=nlstate;i++){
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-               kk1=0.;
+       }
-                 for(j=1; j<=nlstate;j++){
+     }
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
+     /* This for computing probability of death (h=1 means
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-             }
+        as a weighted average of prlim.
+     */
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-           }
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-         }
+     }
-       }
+     /* end probability of death */
-   /******/
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+       for(i=1; i<=nlstate;i++){
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       }
-           nhstepm = nhstepm/hstepm;
+     }
+     fprintf(ficresprobmorprev,"\n");
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+     fprintf(ficresvij,"%.0f ",age );
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     for(i=1; i<=nlstate;i++)
-           for (h=0; h<=nhstepm; h++){
+       for(j=1; j<=nlstate;j++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       }
-             }
+     fprintf(ficresvij,"\n");
-             for(j=1; j<=nlstate+ndeath;j++) {
+     free_matrix(gp,0,nhstepm,1,nlstate);
-               kk1=0.;kk2=0;
+     free_matrix(gm,0,nhstepm,1,nlstate);
-               for(i=1; i<=nlstate;i++) {
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-               }
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   } /* End age */
-             }
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-           }
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-         }
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-       }
+   /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-    }
+   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
-   }
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   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); */
-   if (popforecast==1) {
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-     free_ivector(popage,0,AGESUP);
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-     free_vector(popeffectif,0,AGESUP);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-     free_vector(popcount,0,AGESUP);
+   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));
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   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);
-   fclose(ficrespop);
+   /*  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);
- } /* End of popforecast */
+ */
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
- int fileappend(FILE *fichier, char *optionfich)
+   fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
- {
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   free_vector(xp,1,npar);
-     printf("Problem with file: %s\n", optionfich);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   free_matrix(dnewm,1,nlstate,1,npar);
-     return (0);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   }
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   fflush(fichier);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   return (1);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- }
+   fclose(ficresprobmorprev);
+   fflush(ficgp);
+   fflush(fichtm);
- /**************** function prwizard **********************/
+ }  /* end varevsij */
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
- {
+ /************ Variance of prevlim ******************/
+  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
-   /* Wizard to print covariance matrix template */
+ {
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-   char ca[32], cb[32], cc[32];
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   int numlinepar;
+   double **dnewm,**doldm;
+   int i, j, nhstepm, hstepm;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   double *xp;
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   double *gp, *gm;
-   for(i=1; i <=nlstate; i++){
+   double **gradg, **trgradg;
-     jj=0;
+   double **mgm, **mgp;
-     for(j=1; j <=nlstate+ndeath; j++){
+   double age,agelim;
-       if(j==i) continue;
+   int theta;
-       jj++;
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+   pstamp(ficresvpl);
-       printf("%1d%1d",i,j);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-       fprintf(ficparo,"%1d%1d",i,j);
+   fprintf(ficresvpl,"# Age");
-       for(k=1; k<=ncovmodel;k++){
+   for(i=1; i<=nlstate;i++)
-         /*        printf(" %lf",param[i][j][k]); */
+       fprintf(ficresvpl," %1d-%1d",i,i);
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+   fprintf(ficresvpl,"\n");
-         printf(" 0.");
-         fprintf(ficparo," 0.");
+   xp=vector(1,npar);
-       }
+   dnewm=matrix(1,nlstate,1,npar);
-       printf("\n");
+   doldm=matrix(1,nlstate,1,nlstate);
-       fprintf(ficparo,"\n");
-     }
+   hstepm=1*YEARM; /* Every year of age */
-   }
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   printf("# Scales (for hessian or gradient estimation)\n");
+   agelim = AGESUP;
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   for(i=1; i <=nlstate; i++){
+     if (stepm >= YEARM) hstepm=1;
-     jj=0;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     for(j=1; j <=nlstate+ndeath; j++){
+     gradg=matrix(1,npar,1,nlstate);
-       if(j==i) continue;
+     mgp=matrix(1,npar,1,nlstate);
-       jj++;
+     mgm=matrix(1,npar,1,nlstate);
-       fprintf(ficparo,"%1d%1d",i,j);
+     gp=vector(1,nlstate);
-       printf("%1d%1d",i,j);
+     gm=vector(1,nlstate);
-       fflush(stdout);
-       for(k=1; k<=ncovmodel;k++){
+     for(theta=1; theta <=npar; theta++){
-         /*      printf(" %le",delti3[i][j][k]); */
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         printf(" 0.");
+       }
-         fprintf(ficparo," 0.");
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       }
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       numlinepar++;
+       else
-       printf("\n");
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
-       fprintf(ficparo,"\n");
+       for(i=1;i<=nlstate;i++){
-     }
+         gp[i] = prlim[i][i];
-   }
+         mgp[theta][i] = prlim[i][i];
-   printf("# Covariance matrix\n");
+       }
- /* # 121 Var(a12)\n\ */
+       for(i=1; i<=npar; i++) /* Computes gradient */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+       else
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+       for(i=1;i<=nlstate;i++){
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+         gm[i] = prlim[i][i];
-   fflush(stdout);
+         mgm[theta][i] = prlim[i][i];
-   fprintf(ficparo,"# Covariance matrix\n");
+       }
-   /* # 121 Var(a12)\n\ */
+       for(i=1;i<=nlstate;i++)
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-   /* #   ...\n\ */
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+     } /* End theta */
-   for(itimes=1;itimes<=2;itimes++){
+     trgradg =matrix(1,nlstate,1,npar);
-     jj=0;
-     for(i=1; i <=nlstate; i++){
+     for(j=1; j<=nlstate;j++)
-       for(j=1; j <=nlstate+ndeath; j++){
+       for(theta=1; theta <=npar; theta++)
-         if(j==i) continue;
+         trgradg[j][theta]=gradg[theta][j];
-         for(k=1; k<=ncovmodel;k++){
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-           jj++;
+     /*   printf("\nmgm mgp %d ",(int)age); */
-           ca[0]= k+'a'-1;ca[1]='\0';
+     /*   for(j=1; j<=nlstate;j++){ */
-           if(itimes==1){
+     /*  printf(" %d ",j); */
-             printf("#%1d%1d%d",i,j,k);
+     /*  for(theta=1; theta <=npar; theta++) */
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
-           }else{
+     /*  printf("\n "); */
-             printf("%1d%1d%d",i,j,k);
+     /*   } */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+     /* } */
-             /*  printf(" %.5le",matcov[i][j]); */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
-           }
+     /*   printf("\n gradg %d ",(int)age); */
-           ll=0;
+     /*   for(j=1; j<=nlstate;j++){ */
-           for(li=1;li <=nlstate; li++){
+     /*  printf("%d ",j); */
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+     /*  for(theta=1; theta <=npar; theta++) */
-               if(lj==li) continue;
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
-               for(lk=1;lk<=ncovmodel;lk++){
+     /*  printf("\n "); */
-                 ll++;
+     /*   } */
-                 if(ll<=jj){
+     /* } */
-                   cb[0]= lk +'a'-1;cb[1]='\0';
-                   if(ll<jj){
+     for(i=1;i<=nlstate;i++)
-                     if(itimes==1){
+       varpl[i][(int)age] =0.;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-                     }else{
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-                       printf(" 0.");
+     }else{
-                       fprintf(ficparo," 0.");
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-                     }
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-                   }else{
+     }
-                     if(itimes==1){
+     for(i=1;i<=nlstate;i++)
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-                     }else{
+     fprintf(ficresvpl,"%.0f ",age );
-                       printf(" 0.");
+     for(i=1; i<=nlstate;i++)
-                       fprintf(ficparo," 0.");
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-                     }
+     fprintf(ficresvpl,"\n");
-                   }
+     free_vector(gp,1,nlstate);
-                 }
+     free_vector(gm,1,nlstate);
-               } /* end lk */
+     free_matrix(mgm,1,npar,1,nlstate);
-             } /* end lj */
+     free_matrix(mgp,1,npar,1,nlstate);
-           } /* end li */
+     free_matrix(gradg,1,npar,1,nlstate);
-           printf("\n");
+     free_matrix(trgradg,1,nlstate,1,npar);
-           fprintf(ficparo,"\n");
+   } /* End age */
-           numlinepar++;
-         } /* end k*/
+   free_vector(xp,1,npar);
-       } /*end j */
+   free_matrix(doldm,1,nlstate,1,npar);
-     } /* end i */
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   } /* end itimes */
+ }
- } /* end of prwizard */
- /******************* Gompertz Likelihood ******************************/
+ /************ Variance of one-step probabilities  ******************/
- double gompertz(double x[])
+ 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[])
  {
-   double A,B,L=0.0,sump=0.,num=0.;
+   int i, j=0,  k1, l1, tj;
-   int i,n=0; /* n is the size of the sample */
+   int k2, l2, j1,  z1;
+   int k=0, l;
-   for (i=0;i<=imx-1 ; i++) {
+   int first=1, first1, first2;
-     sump=sump+weight[i];
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-     /*    sump=sump+1;*/
+   double **dnewm,**doldm;
-     num=num+1;
+   double *xp;
-   }
+   double *gp, *gm;
+   double **gradg, **trgradg;
+   double **mu;
-   /* for (i=0; i<=imx; i++)
+   double age, cov[NCOVMAX+1];
-      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]);*/
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   int theta;
-   for (i=1;i<=imx ; i++)
+   char fileresprob[FILENAMELENGTH];
-     {
+   char fileresprobcov[FILENAMELENGTH];
-       if (cens[i] == 1 && wav[i]>1)
+   char fileresprobcor[FILENAMELENGTH];
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   double ***varpij;
-       if (cens[i] == 0 && wav[i]>1)
+   strcpy(fileresprob,"PROB_");
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   strcat(fileresprob,fileres);
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprob);
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-       if (wav[i] > 1 ) { /* ??? */
+   }
-         L=L+A*weight[i];
+   strcpy(fileresprobcov,"PROBCOV_");
-         /*      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]);*/
+   strcat(fileresprobcov,fileresu);
-       }
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     }
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   }
+   strcpy(fileresprobcor,"PROBCOR_");
-   return -2*L*num/sump;
+   strcat(fileresprobcor,fileresu);
- }
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
- /******************* Printing html file ***********/
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+   }
-                   int lastpass, int stepm, int weightopt, char model[],\
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-                   int imx,  double p[],double **matcov,double agemortsup){
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   int i,k;
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   for (i=1;i<=2;i++)
+   pstamp(ficresprob);
-     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(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(ficresprob,"# Age");
-   fprintf(fichtm,"</ul>");
+   pstamp(ficresprobcov);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   fprintf(ficresprobcov,"# Age");
+   pstamp(ficresprobcor);
-  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>");
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcor,"# Age");
-  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]);
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
-   fflush(fichtm);
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
- }
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
- /******************* Gnuplot file **************/
+     }
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+  /* fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
-   char dirfileres[132],optfileres[132];
+   fprintf(ficresprobcor,"\n");
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  */
-   int ng;
+   xp=vector(1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   /*#ifdef windows */
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-     /*#endif */
+   first=1;
+   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   strcpy(dirfileres,optionfilefiname);
+   fprintf(fichtm,"\n");
-   strcpy(optfileres,"vpl");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   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(ficgp, "set ter png small\n set log y\n");
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-   fprintf(ficgp, "set size 0.65,0.65\n");
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- }
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ standard deviations wide on each axis. <br>\
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
- /***********************************************/
- /**************** Main Program *****************/
+   cov[1]=1;
- /***********************************************/
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
- int main(int argc, char *argv[])
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
- {
+   j1=0;
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   for(j1=1; j1<=tj;j1++){
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-   int linei, month, year,iout;
+     /*j1++;*/
-   int jj, ll, li, lj, lk, imk;
+       if  (cptcovn>0) {
-   int numlinepar=0; /* Current linenumber of parameter file */
+         fprintf(ficresprob, "\n#********** Variable ");
-   int itimes;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   int NDIM=2;
+         fprintf(ficresprob, "**********\n#\n");
+         fprintf(ficresprobcov, "\n#********** Variable ");
-   char ca[32], cb[32], cc[32];
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   char dummy[]="                         ";
+         fprintf(ficresprobcov, "**********\n#\n");
-   /*  FILE *fichtm; *//* Html File */
-   /* FILE *ficgp;*/ /*Gnuplot File */
+         fprintf(ficgp, "\n#********** Variable ");
-   struct stat info;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   double agedeb, agefin,hf;
+         fprintf(ficgp, "**********\n#\n");
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   double fret;
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-   double **xi,tmp,delta;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-   double dum; /* Dummy variable */
-   double ***p3mat;
+         fprintf(ficresprobcor, "\n#********** Variable ");
-   double ***mobaverage;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   int *indx;
+         fprintf(ficresprobcor, "**********\n#");
-   char line[MAXLINE], linepar[MAXLINE];
+       }
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char pathr[MAXLINE], pathimach[MAXLINE];
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-   char **bp, *tok, *val; /* pathtot */
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   int firstobs=1, lastobs=10;
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-   int sdeb, sfin; /* Status at beginning and end */
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-   int c,  h , cpt,l;
+       for (age=bage; age<=fage; age ++){
-   int ju,jl, mi;
+         cov[2]=age;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+         if(nagesqr==1)
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+           cov[3]= age*age;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+         for (k=1; k<=cptcovn;k++) {
-   int mobilav=0,popforecast=0;
+           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-   int hstepm, nhstepm;
+           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-   int agemortsup;
+                                                          * 1  1 1 1 1
-   float  sumlpop=0.;
+                                                          * 2  2 1 1 1
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+                                                          * 3  1 2 1 1
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+                                                          */
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-   double bage, fage, age, agelim, agebase;
+         }
-   double ftolpl=FTOL;
+         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   double **prlim;
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   double *severity;
+         for (k=1; k<=cptcovprod;k++)
-   double ***param; /* Matrix of parameters */
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-   double  *p;
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
+         for(theta=1; theta <=npar; theta++){
-   double *delti; /* Scale */
+           for(i=1; i<=npar; i++)
-   double ***eij, ***vareij;
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-   double **varpl; /* Variances of prevalence limits by age */
-   double *epj, vepp;
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+           k=0;
-   double **ximort;
+           for(i=1; i<= (nlstate); i++){
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+             for(j=1; j<=(nlstate+ndeath);j++){
-   int *dcwave;
+               k=k+1;
+               gp[k]=pmmij[i][j];
-   char z[1]="c", occ;
+             }
+           }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
+           for(i=1; i<=npar; i++)
-   char *stratrunc;
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-   int lstra;
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   long total_usecs;
+           k=0;
+           for(i=1; i<=(nlstate); i++){
- /*   setlocale (LC_ALL, ""); */
+             for(j=1; j<=(nlstate+ndeath);j++){
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+               k=k+1;
- /*   textdomain (PACKAGE); */
+               gm[k]=pmmij[i][j];
- /*   setlocale (LC_CTYPE, ""); */
+             }
- /*   setlocale (LC_MESSAGES, ""); */
+           }
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-   (void) gettimeofday(&start_time,&tzp);
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-   curr_time=start_time;
+         }
-   tm = *localtime(&start_time.tv_sec);
-   tmg = *gmtime(&start_time.tv_sec);
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-   strcpy(strstart,asctime(&tm));
+           for(theta=1; theta <=npar; theta++)
+             trgradg[j][theta]=gradg[theta][j];
- /*  printf("Localtime (at start)=%s",strstart); */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
- /*  tm = *localtime(&start_time.tv_sec); */
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
- /*   tp.tv_sec = mktime(&tmg); */
+         k=0;
- /*   strt=asctime(&tmg); */
+         for(i=1; i<=(nlstate); i++){
- /*   printf("Time(after) =%s",strstart);  */
+           for(j=1; j<=(nlstate+ndeath);j++){
- /*  (void) time (&time_value);
+             k=k+1;
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+             mu[k][(int) age]=pmmij[i][j];
- *  tm = *localtime(&time_value);
+           }
- *  strstart=asctime(&tm);
+         }
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
- */
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             varpij[i][j][(int)age] = doldm[i][j];
-   nberr=0; /* Number of errors and warnings */
-   nbwarn=0;
+         /*printf("\n%d ",(int)age);
-   getcwd(pathcd, size);
+           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]));
-   printf("\n%s\n%s",version,fullversion);
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-   if(argc <=1){
+           }*/
-     printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+         fprintf(ficresprob,"\n%d ",(int)age);
-     i=strlen(pathr);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-     if(pathr[i-1]=='\n')
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-       pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-       printf("Pathr |%s|\n",pathr);
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       printf("val= |%s| pathr=%s\n",val,pathr);
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-       strcpy (pathtot, val);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-       if(pathr[0] == '\0') break; /* Dirty */
+         }
-     }
+         i=0;
-   }
+         for (k=1; k<=(nlstate);k++){
-   else{
+           for (l=1; l<=(nlstate+ndeath);l++){
-     strcpy(pathtot,argv[1]);
+             i++;
-   }
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   /*cygwin_split_path(pathtot,path,optionfile);
+             for (j=1; j<=i;j++){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-   /* cutv(path,optionfile,pathtot,'\\');*/
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-   /* 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);
+         }/* end of loop for state */
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+       } /* end of loop for age */
-  /*   strcpy(pathimach,argv[0]); */
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+       /* Confidence intervalle of pij  */
-     printf("Current directory %s!\n",pathcd);
+       /*
-   strcpy(command,"mkdir ");
+         fprintf(ficgp,"\nunset parametric;unset label");
-   strcat(command,optionfilefiname);
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   if((outcmd=system(command)) != 0){
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-     /* fclose(ficlog); */
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
- /*     exit(1); */
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-   }
+       */
- /*   if((imk=mkdir(optionfilefiname))<0){ */
- /*     perror("mkdir"); */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
- /*   } */
+       first1=1;first2=2;
+       for (k2=1; k2<=(nlstate);k2++){
-   /*-------- arguments in the command line --------*/
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
-   /* Log file */
+           j=(k2-1)*(nlstate+ndeath)+l2;
-   strcat(filelog, optionfilefiname);
+           for (k1=1; k1<=(nlstate);k1++){
-   strcat(filelog,".log");    /* */
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+               if(l1==k1) continue;
-     printf("Problem with logfile %s\n",filelog);
+               i=(k1-1)*(nlstate+ndeath)+l1;
-     goto end;
+               if(i<=j) continue;
-   }
+               for (age=bage; age<=fage; age ++){
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+                 if ((int)age %5==0){
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-  path=%s \n\
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-  optionfile=%s\n\
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-  optionfilext=%s\n\
+                   c12=cv12/sqrt(v1*v2);
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+                   /* Computing eigen value of matrix of covariance */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   printf("Local time (at start):%s",strstart);
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+                   if ((lc2 <0) || (lc1 <0) ){
-   fflush(ficlog);
+                     if(first2==1){
- /*   (void) gettimeofday(&curr_time,&tzp); */
+                       first1=0;
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     }
-   /* */
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-   strcpy(fileres,"r");
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-   strcat(fileres, optionfilefiname);
+                     /* lc2=fabs(lc2); */
-   strcat(fileres,".txt");    /* Other files have txt extension */
+                   }
-   /*---------arguments file --------*/
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-     printf("Problem with optionfile %s\n",optionfile);
+                   v21=(lc1-v1)/cv12*v11;
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+                   v12=-v21;
-     fflush(ficlog);
+                   v22=v11;
-     goto end;
+                   tnalp=v21/v11;
-   }
+                   if(first1==1){
+                     first1=0;
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   }
-   strcpy(filereso,"o");
+                   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);
-   strcat(filereso,fileres);
+                   /*printf(fignu*/
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-     printf("Problem with Output resultfile: %s\n", filereso);
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+                   if(first==1){
-     fflush(ficlog);
+                     first=0;
-     goto end;
+                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
-   }
+                     fprintf(ficgp,"\nset parametric;unset label");
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-   /* Reads comments: lines beginning with '#' */
+                     fprintf(ficgp,"\nset ter svg size 640, 480");
-   numlinepar=0;
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-   while((c=getc(ficpar))=='#' && c!= EOF){
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
-     ungetc(c,ficpar);
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
-     fgets(line, MAXLINE, ficpar);
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
-     numlinepar++;
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-     puts(line);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-     fputs(line,ficparo);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-     fputs(line,ficlog);
+                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-   }
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   ungetc(c,ficpar);
+                     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",\
-   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);
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   numlinepar++;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   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);
+                   }else{
-   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);
+                     first=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);
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-   fflush(ficlog);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-     ungetc(c,ficpar);
+                     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",\
-     fgets(line, MAXLINE, ficpar);
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-     numlinepar++;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-     puts(line);
+                   }/* if first */
-     fputs(line,ficparo);
+                 } /* age mod 5 */
-     fputs(line,ficlog);
+               } /* 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);
-   ungetc(c,ficpar);
+               first=1;
+             } /*l12 */
+           } /* k12 */
-   covar=matrix(0,NCOVMAX,1,n);
+         } /*l1 */
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       }/* k1 */
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       /* } */ /* loop covariates */
+   }
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   free_vector(xp,1,npar);
-   delti=delti3[1][1];
+   fclose(ficresprob);
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   fclose(ficresprobcov);
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+   fclose(ficresprobcor);
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+   fflush(ficgp);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   fflush(fichtmcov);
-     fprintf(ficlog," You choose 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);
+ /******************* Printing html file ***********/
-     goto end;
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
-     exit(0);
+                   int lastpass, int stepm, int weightopt, char model[],\
-   }
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   else if(mle==-3) {
+                   int popforecast, int prevfcast, int estepm ,          \
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+                   double jprev1, double mprev1,double anprev1, double dateprev1, \
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+                   double jprev2, double mprev2,double anprev2, double dateprev2){
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+   int jj1, k1, i1, cpt;
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     matcov=matrix(1,npar,1,npar);
+    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 \
-   else{
+ </ul>");
-     /* Read guess parameters */
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
-     /* Reads comments: lines beginning with '#' */
+    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",
-     while((c=getc(ficpar))=='#' && c!= EOF){
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
-       ungetc(c,ficpar);
+    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) ",
-       fgets(line, MAXLINE, ficpar);
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
-       numlinepar++;
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
-       puts(line);
+    fprintf(fichtm,"\
-       fputs(line,ficparo);
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-       fputs(line,ficlog);
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
-     }
+    fprintf(fichtm,"\
-     ungetc(c,ficpar);
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+    fprintf(fichtm,"\
-     for(i=1; i <=nlstate; i++){
+  - (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): \
-       j=0;
+    <a href=\"%s\">%s</a> <br>\n",
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
-         if(jj==i) continue;
+    if(prevfcast==1){
-         j++;
+      fprintf(fichtm,"\
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+  - Prevalence projections by age and states:                            \
-         if ((i1 != i) && (j1 != j)){
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
-           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);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-           exit(1);
-         }
+  m=pow(2,cptcoveff);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-         if(mle==1)
-           printf("%1d%1d",i,j);
+  jj1=0;
-         fprintf(ficlog,"%1d%1d",i,j);
+  for(k1=1; k1<=m;k1++){
-         for(k=1; k<=ncovmodel;k++){
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-           fscanf(ficpar," %lf",&param[i][j][k]);
+      jj1++;
-           if(mle==1){
+      if (cptcovn > 0) {
-             printf(" %lf",param[i][j][k]);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-             fprintf(ficlog," %lf",param[i][j][k]);
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-           }
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-           else
+          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
-             fprintf(ficlog," %lf",param[i][j][k]);
+        }
-           fprintf(ficparo," %lf",param[i][j][k]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-         }
+      }
-         fscanf(ficpar,"\n");
+      /* aij, bij */
-         numlinepar++;
+      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> \
-         if(mle==1)
+ <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-           printf("\n");
+      /* Pij */
-         fprintf(ficlog,"\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> \
-         fprintf(ficparo,"\n");
+ <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-       }
+      /* Quasi-incidences */
-     }
+      fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-     fflush(ficlog);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
-     p=param[1][1];
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-     /* Reads comments: lines beginning with '#' */
+      /* Survival functions (period) in state j */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      for(cpt=1; cpt<=nlstate;cpt++){
-       ungetc(c,ficpar);
+        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> \
-       fgets(line, MAXLINE, ficpar);
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
-       numlinepar++;
+      }
-       puts(line);
+      /* State specific survival functions (period) */
-       fputs(line,ficparo);
+      for(cpt=1; cpt<=nlstate;cpt++){
-       fputs(line,ficlog);
+        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.\
-     ungetc(c,ficpar);
+  <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);
+      }
-     for(i=1; i <=nlstate; i++){
+      /* Period (stable) prevalence in each health state */
-       for(j=1; j <=nlstate+ndeath-1; j++){
+      for(cpt=1; cpt<=nlstate;cpt++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+        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> \
-         if ((i1-i)*(j1-j)!=0){
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+      }
-           exit(1);
+     if(prevfcast==1){
-         }
+       /* Projection of prevalence up to period (stable) prevalence in each health state */
-         printf("%1d%1d",i,j);
+       for(cpt=1; cpt<=nlstate;cpt++){
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         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,"%1d%1d",i1,j1);
+ <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);
-         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]);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-           fprintf(ficlog," %le",delti3[i][j][k]);
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
-         }
+ <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
-         fscanf(ficpar,"\n");
+      }
-         numlinepar++;
+    /* } /\* end i1 *\/ */
-         printf("\n");
+  }/* End k1 */
-         fprintf(ficparo,"\n");
+  fprintf(fichtm,"</ul>");
-         fprintf(ficlog,"\n");
-       }
+  fprintf(fichtm,"\
-     }
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-     fflush(ficlog);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
-     delti=delti3[1][1];
+ But because parameters are usually highly correlated (a higher incidence of disability \
+ and a higher incidence of recovery can give very close observed transition) it might \
+ be very useful to look not only at linear confidence intervals estimated from the \
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
-     /* Reads comments: lines beginning with '#' */
+ covariance matrix of the one-step probabilities. \
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       numlinepar++;
+          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-       puts(line);
+  fprintf(fichtm,"\
-       fputs(line,ficparo);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       fputs(line,ficlog);
+          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-     }
-     ungetc(c,ficpar);
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     matcov=matrix(1,npar,1,npar);
+          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-     for(i=1; i <=npar; i++){
+  fprintf(fichtm,"\
-       fscanf(ficpar,"%s",&str);
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
-       if(mle==1)
+    <a href=\"%s\">%s</a> <br>\n</li>",
-         printf("%s",str);
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
-       fprintf(ficlog,"%s",str);
+  fprintf(fichtm,"\
-       fprintf(ficparo,"%s",str);
+  - (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): \
-       for(j=1; j <=i; j++){
+    <a href=\"%s\">%s</a> <br>\n</li>",
-         fscanf(ficpar," %le",&matcov[i][j]);
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-         if(mle==1){
+  fprintf(fichtm,"\
-           printf(" %.5le",matcov[i][j]);
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-         }
+          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-         fprintf(ficlog," %.5le",matcov[i][j]);
+  fprintf(fichtm,"\
-         fprintf(ficparo," %.5le",matcov[i][j]);
+  - 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_"));
-       fscanf(ficpar,"\n");
+  fprintf(fichtm,"\
-       numlinepar++;
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-       if(mle==1)
+          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
-         printf("\n");
-       fprintf(ficlog,"\n");
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-       fprintf(ficparo,"\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 */
-     for(i=1; i <=npar; i++)
+ /*      <br>",fileres,fileres,fileres,fileres); */
-       for(j=i+1;j<=npar;j++)
+ /*  else  */
-         matcov[i][j]=matcov[j][i];
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+  fflush(fichtm);
-     if(mle==1)
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-       printf("\n");
-     fprintf(ficlog,"\n");
+  m=pow(2,cptcoveff);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-     fflush(ficlog);
+  jj1=0;
-     /*-------- Rewriting parameter file ----------*/
+  for(k1=1; k1<=m;k1++){
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+      jj1++;
-     strcat(rfileres,".");    /* */
+      if (cptcovn > 0) {
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-     }
+      }
-     fprintf(ficres,"#%s\n",version);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-   }    /* End of mle != -3 */
+        fprintf(fichtm,"<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 <br>\
-   /*-------- data file ----------*/
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
-   if((fic=fopen(datafile,"r"))==NULL)    {
+      }
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-   }
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
-   n= lastobs;
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg<br>\
-   severity = vector(1,maxwav);
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-   outcome=imatrix(1,maxwav+1,1,n);
+    /* } /\* end i1 *\/ */
-   num=lvector(1,n);
+  }/* End k1 */
-   moisnais=vector(1,n);
+  fprintf(fichtm,"</ul>");
-   annais=vector(1,n);
+  fflush(fichtm);
-   moisdc=vector(1,n);
+ }
-   andc=vector(1,n);
-   agedc=vector(1,n);
+ /******************* Gnuplot file **************/
-   cod=ivector(1,n);
+     void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
-   weight=vector(1,n);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   char dirfileres[132],optfileres[132];
-   mint=matrix(1,maxwav,1,n);
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   anint=matrix(1,maxwav,1,n);
+   int lv=0, vlv=0, kl=0;
-   s=imatrix(1,maxwav+1,1,n);
+   int ng=0;
-   tab=ivector(1,NCOVMAX);
+   int vpopbased;
-   ncodemax=ivector(1,8);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   i=1;
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-   linei=0;
+ /*   } */
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     linei=linei+1;
+   /*#ifdef windows */
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-       if(line[j] == '\t')
+     /*#endif */
-         line[j] = ' ';
+   m=pow(2,cptcoveff);
-     }
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   /* Contribution to likelihood */
-       ;
+   /* Plot the probability implied in the likelihood */
-     };
+     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
-     line[j+1]=0;  /* Trims blanks at end of line */
+     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
-     if(line[0]=='#'){
+     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
-       fprintf(ficlog,"Comment line\n%s\n",line);
+     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
-       printf("Comment line\n%s\n",line);
+ /* nice for mle=4 plot by number of matrix products.
-       continue;
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
-     }
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
-     for (j=maxwav;j>=1;j--){
+     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
-       cutv(stra, strb,line,' ');
+     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));
-       errno=0;
+     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
-       lval=strtol(strb,&endptr,10);
+     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));
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     for (i=1; i<= nlstate ; i ++) {
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
-         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);
+       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
-         exit(1);
+       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
-       }
+       for (j=2; j<= nlstate+ndeath ; j ++) {
-       s[j][i]=lval;
+         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);
+       }
-       strcpy(line,stra);
+       fprintf(ficgp,";\nset out; unset ylabel;\n");
-       cutv(stra, strb,line,' ');
+     }
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
-       }
+     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
-       else  if(iout=sscanf(strb,"%s.") != 0){
+     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
-         month=99;
+     fprintf(ficgp,"\nset out;unset log\n");
-         year=9999;
+     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
-       }else{
-         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);
+   strcpy(dirfileres,optionfilefiname);
-         exit(1);
+   strcpy(optfileres,"vpl");
-       }
+  /* 1eme*/
-       anint[j][i]= (double) year;
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-       mint[j][i]= (double)month;
+     for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
-       strcpy(line,stra);
+       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-     } /* ENd Waves */
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     cutv(stra, strb,line,' ');
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-     }
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       month=99;
+         vlv= nbcode[Tvaraff[lv]][lv];
-       year=9999;
+         fprintf(ficgp," V%d=%d ",k,vlv);
-     }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);
+       fprintf(ficgp,"\n#\n");
-       exit(1);
-     }
+      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
-     andc[i]=(double) year;
+      fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
-     moisdc[i]=(double) month;
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-     strcpy(line,stra);
+ set ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n\
-     cutv(stra, strb,line,' ');
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     }
+      for (i=1; i<= nlstate ; i ++) {
-     else  if(iout=sscanf(strb,"%s.") != 0){
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       month=99;
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-       year=9999;
+      }
-     }else{
+      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);
-       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);
+      for (i=1; i<= nlstate ; i ++) {
-       exit(1);
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     }
+        else fprintf(ficgp," %%*lf (%%*lf)");
-     annais[i]=(double)(year);
+      }
-     moisnais[i]=(double)(month);
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-     strcpy(line,stra);
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     cutv(stra, strb,line,' ');
+        else fprintf(ficgp," %%*lf (%%*lf)");
-     errno=0;
+      }
-     dval=strtod(strb,&endptr);
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-     if( strb[0]=='\0' || (*endptr != '\0')){
+      fprintf(ficgp,"\nset out \n");
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+     } /* k1 */
-       exit(1);
+   } /* cpt */
-     }
+   /*2 eme*/
-     weight[i]=dval;
+   for (k1=1; k1<= m ; k1 ++) {
-     strcpy(line,stra);
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     for (j=ncovcol;j>=1;j--){
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-       cutv(stra, strb,line,' ');
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       errno=0;
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       lval=strtol(strb,&endptr,10);
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       if( strb[0]=='\0' || (*endptr != '\0')){
+         vlv= nbcode[Tvaraff[lv]][lv];
-         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);
+         fprintf(ficgp," V%d=%d ",k,vlv);
-         exit(1);
+       }
-       }
+       fprintf(ficgp,"\n#\n");
-       if(lval <-1 || lval >1){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+       if(vpopbased==0)
-  For example, for multinomial values like 1, 2 and 3,\n \
+         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-  build V1=0 V2=0 for the reference value (1),\n \
+       else
-         V1=1 V2=0 for (2) \n \
+         fprintf(ficgp,"\nreplot ");
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+       for (i=1; i<= nlstate+1 ; i ++) {
-  output of IMaCh is often meaningless.\n \
+         k=2*i;
-  Exiting.\n",lval,linei, i,line,j);
+         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);
-         exit(1);
+         for (j=1; j<= nlstate+1 ; j ++) {
-       }
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       covar[j][i]=(double)(lval);
+           else fprintf(ficgp," %%*lf (%%*lf)");
-       strcpy(line,stra);
+         }
-     }
+         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-     lstra=strlen(stra);
+         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+         for (j=1; j<= nlstate+1 ; j ++) {
-       stratrunc = &(stra[lstra-9]);
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       num[i]=atol(stratrunc);
+           else fprintf(ficgp," %%*lf (%%*lf)");
-     }
+         }
-     else
+         fprintf(ficgp,"\" t\"\" w l lt 0,");
-       num[i]=atol(stra);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+         for (j=1; j<= nlstate+1 ; j ++) {
-       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;}*/
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
-     i=i+1;
+         }
-   } /* End loop reading  data */
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-   fclose(fic);
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-   /* printf("ii=%d", ij);
+       } /* state */
-      scanf("%d",i);*/
+     } /* vpopbased */
-   imx=i-1; /* Number of individuals */
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+   } /* k1 */
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   /*3eme*/
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+   for (k1=1; k1<= m ; k1 ++) {
-     }*/
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-    /*  for (i=1; i<=imx; i++){
+       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
-      if (s[4][i]==9)  s[4][i]=-1;
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-      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]));}*/
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-   /* for (i=1; i<=imx; i++) */
+         /* 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 */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+         vlv= nbcode[Tvaraff[lv]][lv];
-      else weight[i]=1;*/
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
-   /* Calculation of the number of parameters from char model */
+       fprintf(ficgp,"\n#\n");
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
-   Tprod=ivector(1,15);
+       /*       k=2+nlstate*(2*cpt-2); */
-   Tvaraff=ivector(1,15);
+       k=2+(nlstate+1)*(cpt-1);
-   Tvard=imatrix(1,15,1,2);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-   Tage=ivector(1,15);
+       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);
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     j=0, j1=0, k1=1, k2=1;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-     j=nbocc(model,'+'); /* j=Number of '+' */
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     cptcovn=j+1;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-     cptcovprod=j1; /*Number of products */
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     strcpy(modelsav,model);
+       */
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+       for (i=1; i< nlstate ; i ++) {
-       printf("Error. Non available option model=%s ",model);
+         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(ficlog,"Error. Non available option model=%s ",model);
+         /*      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);*/
-       goto end;
-     }
+       }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
-     /* This loop fills the array Tvar from the string 'model'.*/
+     }
+   }
-     for(i=(j+1); i>=1;i--){
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+   /* Survival functions (period) from state i in state j by initial state i */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-       /*scanf("%d",i);*/
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       if (strchr(strb,'*')) {  /* Model includes a product */
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-           cptcovprod--;
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-           cutv(strb,stre,strd,'V');
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+         vlv= nbcode[Tvaraff[lv]][lv];
-           cptcovage++;
+         fprintf(ficgp," V%d=%d ",k,vlv);
-             Tage[cptcovage]=i;
+       }
-             /*printf("stre=%s ", stre);*/
+       fprintf(ficgp,"\n#\n");
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
-           cptcovprod--;
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-           cutv(strb,stre,strc,'V');
+ set ter svg size 640, 480\n\
-           Tvar[i]=atoi(stre);
+ unset log y\n\
-           cptcovage++;
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-           Tage[cptcovage]=i;
+       k=3;
-         }
+       for (i=1; i<= nlstate ; i ++){
-         else {  /* Age is not in the model */
+         if(i==1)
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-           Tvar[i]=ncovcol+k1;
+         else
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           fprintf(ficgp,", '' ");
-           Tprod[k1]=i;
+         l=(nlstate+ndeath)*(i-1)+1;
-           Tvard[k1][1]=atoi(strc); /* m*/
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-           Tvard[k1][2]=atoi(stre); /* n */
+         for (j=2; j<= nlstate+ndeath ; j ++)
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+           fprintf(ficgp,"+$%d",k+l+j-1);
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
-           for (k=1; k<=lastobs;k++)
+       } /* nlstate */
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+       fprintf(ficgp,"\nset out\n");
-           k1++;
+     } /* end cpt state*/
-           k2=k2+2;
+   } /* end covariate */
-         }
-       }
+   /* Survival functions (period) from state i in state j by final state j */
-       else { /* no more sum */
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
-        /*  scanf("%d",i);*/
+       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);
-       cutv(strd,strc,strb,'V');
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       Tvar[i]=atoi(strc);
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-       }
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       strcpy(modelsav,stra);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         scanf("%d",i);*/
+         vlv= nbcode[Tvaraff[lv]][lv];
-     } /* end of loop + */
+         fprintf(ficgp," V%d=%d ",k,vlv);
-   } /* end model */
+       }
+       fprintf(ficgp,"\n#\n");
-   /*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*/
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ set ter svg size 640, 480\n\
-   printf("cptcovprod=%d ", cptcovprod);
+ unset log y\n\
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3;
-   scanf("%d ",i);*/
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+         if(j==1)
-     /*  if(mle==1){*/
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-   if (weightopt != 1) { /* Maximisation without weights*/
+         else
-     for(i=1;i<=n;i++) weight[i]=1.0;
+           fprintf(ficgp,", '' ");
-   }
+         l=(nlstate+ndeath)*(cpt-1) +j;
-     /*-calculation of age at interview from date of interview and age at death -*/
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-   agev=matrix(1,maxwav,1,imx);
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-   for (i=1; i<=imx; i++) {
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-     for(m=2; (m<= maxwav); m++) {
+       } /* nlstate */
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       fprintf(ficgp,", '' ");
-         anint[m][i]=9999;
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-         s[m][i]=-1;
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       }
+         l=(nlstate+ndeath)*(cpt-1) +j;
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         if(j < nlstate)
-         nberr++;
+           fprintf(ficgp,"$%d +",k+l);
-         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);
+         else
-         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);
+           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-         s[m][i]=-1;
+       }
-       }
+       fprintf(ficgp,"\nset out\n");
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+     } /* end cpt state*/
-         nberr++;
+   } /* end covariate */
-         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]);
+   /* CV preval stable (period) for each covariate */
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
-       }
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-     }
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
-   }
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-   for (i=1; i<=imx; i++)  {
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-     for(m=firstpass; (m<= lastpass); m++){
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         vlv= nbcode[Tvaraff[lv]][lv];
-         if (s[m][i] >= nlstate+1) {
+         fprintf(ficgp," V%d=%d ",k,vlv);
-           if(agedc[i]>0)
+       }
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+       fprintf(ficgp,"\n#\n");
-               agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
-             else {
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-               if ((int)andc[i]!=9999){
+ set ter svg size 640, 480\n\
-                 nbwarn++;
+ unset log y\n\
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+       k=3; /* Offset */
-                 agev[m][i]=-1;
+       for (i=1; i<= nlstate ; i ++){
-               }
+         if(i==1)
-             }
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         }
+         else
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+           fprintf(ficgp,", '' ");
-                                  years but with the precision of a month */
+         l=(nlstate+ndeath)*(i-1)+1;
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+         for (j=2; j<= nlstate ; j ++)
-             agev[m][i]=1;
+           fprintf(ficgp,"+$%d",k+l+j-1);
-           else if(agev[m][i] <agemin){
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-             agemin=agev[m][i];
+       } /* nlstate */
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+       fprintf(ficgp,"\nset out\n");
-           }
+     } /* end cpt state*/
-           else if(agev[m][i] >agemax){
+   } /* end covariate */
-             agemax=agev[m][i];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   if(prevfcast==1){
-           }
+   /* Projection from cross-sectional to stable (period) for each covariate */
-           /*agev[m][i]=anint[m][i]-annais[i];*/
-           /*     agev[m][i] = age[i]+2*m;*/
+     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 */
-         else { /* =9 */
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
-           agev[m][i]=1;
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
-           s[m][i]=-1;
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-         }
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       }
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       else /*= 0 Unknown */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         agev[m][i]=1;
+           vlv= nbcode[Tvaraff[lv]][lv];
-     }
+           fprintf(ficgp," V%d=%d ",k,vlv);
+         }
-   }
+         fprintf(ficgp,"\n#\n");
-   for (i=1; i<=imx; i++)  {
-     for(m=firstpass; (m<=lastpass); m++){
+         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
-       if (s[m][i] > (nlstate+ndeath)) {
+         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
-         nberr++;
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
-         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);
+ set ter svg size 640, 480\n\
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+ unset log y\n\
-         goto end;
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-       }
+         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
-     }
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-   }
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-   /*for (i=1; i<=imx; i++){
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-   for (m=firstpass; (m<lastpass); m++){
+           if(i==1){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
- }
+           }else{
+             fprintf(ficgp,",\\\n '' ");
- }*/
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             fprintf(ficgp," u 2:("); /* Age is in 2 */
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             if(i==nlstate+1)
-   agegomp=(int)agemin;
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
-   free_vector(severity,1,maxwav);
++(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,cpt );
-   free_imatrix(outcome,1,maxwav+1,1,n);
+             else
-   free_vector(moisnais,1,n);
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
-   free_vector(annais,1,n);
++(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-   /* free_matrix(mint,1,maxwav,1,n);
+           }else{
-      free_matrix(anint,1,maxwav,1,n);*/
+             fprintf(ficgp,"u 6:(("); /* Age is in 6 */
-   free_vector(moisdc,1,n);
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-   free_vector(andc,1,n);
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             kl=0;
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate  */
-   wav=ivector(1,imx);
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               vlv= nbcode[Tvaraff[lv]][lv];
-   /* Concatenates waves */
+               kl++;
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+               /* 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 */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+               /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/
-   Tcode=ivector(1,100);
+               if(k==cptcoveff)
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+                 if(i==nlstate+1)
-   ncodemax[1]=1;
+                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
++(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                 else
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
-                                  the estimations*/
++(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-   h=0;
+               else{
-   m=pow(2,cptcoveff);
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
+                 kl++;
-   for(k=1;k<=cptcoveff; k++){
+               }
-     for(i=1; i <=(m/pow(2,k));i++){
+             } /* end covariate */
-       for(j=1; j <= ncodemax[k]; j++){
+           } /* end if covariate */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         } /* nlstate */
-           h++;
+         fprintf(ficgp,"\nset out\n");
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+       } /* end cpt state*/
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+     } /* end covariate */
-         }
+   } /* End if prevfcast */
-       }
-     }
-   }
+   /* proba elementaires */
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
-      codtab[1][2]=1;codtab[2][2]=2; */
+   for(i=1,jk=1; i <=nlstate; i++){
-   /* for(i=1; i <=m ;i++){
+     fprintf(ficgp,"# initial state %d\n",i);
-      for(k=1; k <=cptcovn; k++){
+     for(k=1; k <=(nlstate+ndeath); k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+       if (k != i) {
-      }
+         fprintf(ficgp,"#   current state %d\n",k);
-      printf("\n");
+         for(j=1; j <=ncovmodel; j++){
-      }
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-      scanf("%d",i);*/
+           jk++;
+         }
-   /*------------ gnuplot -------------*/
+         fprintf(ficgp,"\n");
-   strcpy(optionfilegnuplot,optionfilefiname);
+       }
-   if(mle==-3)
+     }
-     strcat(optionfilegnuplot,"-mort");
+    }
-   strcat(optionfilegnuplot,".gp");
+   fprintf(ficgp,"##############\n#\n");
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   /*goto avoid;*/
-     printf("Problem with file %s",optionfilegnuplot);
+   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{
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-     fprintf(ficgp,"\n# %s\n", version);
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-     fprintf(ficgp,"set missing 'NaNq'\n");
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-   }
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-   /*  fclose(ficgp);*/
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-   /*--------- index.htm --------*/
+   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");
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-   if(mle==-3)
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
-     strcat(optionfilehtm,"-mort");
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
-   strcat(optionfilehtm,".htm");
+   fprintf(ficgp,"#\n");
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+      fprintf(ficgp,"# ng=%d\n",ng);
-   }
+      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+      for(jk=1; jk <=m; jk++) {
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+        fprintf(ficgp,"#    jk=%d\n",jk);
-   strcat(optionfilehtmcov,"-cov.htm");
+        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+        fprintf(ficgp,"\nset ter svg size 640, 480 ");
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+        if (ng==1){
-   }
+          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
-   else{
+          fprintf(ficgp,"\nunset log y");
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+        }else if (ng==2){
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+          fprintf(ficgp,"\nset log y");
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+        }else if (ng==3){
-   }
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+          fprintf(ficgp,"\nset log y");
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+        }else
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+          fprintf(ficgp,"\nunset title ");
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
- \n\
+        i=1;
- <hr  size=\"2\" color=\"#EC5E5E\">\
+        for(k2=1; k2<=nlstate; k2++) {
-  <ul><li><h4>Parameter files</h4>\n\
+          k3=i;
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+          for(k=1; k<=(nlstate+ndeath); k++) {
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+            if (k != k2){
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+              switch( ng) {
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+              case 1:
-  - Date and time at start: %s</ul>\n",\
+                if(nagesqr==0)
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+                  fprintf(ficgp," p%d+p%d*x",i,i+1);
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+                else /* nagesqr =1 */
-           fileres,fileres,\
+                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+                break;
-   fflush(fichtm);
+              case 2: /* ng=2 */
+                if(nagesqr==0)
-   strcpy(pathr,path);
+                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-   strcat(pathr,optionfilefiname);
+                else /* nagesqr =1 */
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+                break;
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+              case 3:
-      and prints on file fileres'p'. */
+                if(nagesqr==0)
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+                else /* nagesqr =1 */
-   fprintf(fichtm,"\n");
+                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+                break;
- 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",\
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-           imx,agemin,agemax,jmin,jmax,jmean);
+              for(j=3; j <=ncovmodel-nagesqr; j++) {
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                if(ij <=cptcovage) { /* Bug valgrind */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                  if((j-2)==Tage[ij]) { /* Bug valgrind */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                    ij++;
+                  }
-   /* 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] */
+                else
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+              }
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+              if(ng != 1){
+                fprintf(ficgp,")/(1");
-   if (mle==-3){
-     ximort=matrix(1,NDIM,1,NDIM);
+                for(k1=1; k1 <=nlstate; k1++){
-     cens=ivector(1,n);
+                  if(nagesqr==0)
-     ageexmed=vector(1,n);
+                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-     agecens=vector(1,n);
+                  else /* nagesqr =1 */
-     dcwave=ivector(1,n);
+                    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);
-     for (i=1; i<=imx; i++){
+                  ij=1;
-       dcwave[i]=-1;
+                  for(j=3; j <=ncovmodel-nagesqr; j++){
-       for (m=firstpass; m<=lastpass; m++)
+                    if(ij <=cptcovage) { /* Bug valgrind */
-         if (s[m][i]>nlstate) {
+                      if((j-2)==Tage[ij]) { /* Bug valgrind */
-           dcwave[i]=m;
+                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+                        /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-           break;
+                        ij++;
-         }
+                      }
-     }
+                    }
+                    else
-     for (i=1; i<=imx; i++) {
+                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-       if (wav[i]>0){
+                  }
-         ageexmed[i]=agev[mw[1][i]][i];
+                  fprintf(ficgp,")");
-         j=wav[i];
+                }
-         agecens[i]=1.;
+                fprintf(ficgp,")");
+                if(ng ==2)
-         if (ageexmed[i]> 1 && wav[i] > 0){
+                  fprintf(ficgp," t \"p%d%d\" ", k2,k);
-           agecens[i]=agev[mw[j][i]][i];
+                else /* ng= 3 */
-           cens[i]= 1;
+                  fprintf(ficgp," t \"i%d%d\" ", k2,k);
-         }else if (ageexmed[i]< 1)
+              }else{ /* end ng <> 1 */
-           cens[i]= -1;
+                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+              }
-           cens[i]=0 ;
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-       }
+              i=i+ncovmodel;
-       else cens[i]=-1;
+            }
-     }
+          } /* end k */
+        } /* end k2 */
-     for (i=1;i<=NDIM;i++) {
+        fprintf(ficgp,"\n set out\n");
-       for (j=1;j<=NDIM;j++)
+      } /* end jk */
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+    } /* end ng */
-     }
+  /* avoid: */
+    fflush(ficgp);
-     p[1]=0.0268; p[NDIM]=0.083;
+ }  /* end gnuplot */
-     /*printf("%lf %lf", p[1], p[2]);*/
+ /*************** Moving average **************/
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
+   int i, cpt, cptcod;
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   int modcovmax =1;
-       printf("Problem with resultfile: %s\n", filerespow);
+   int mobilavrange, mob;
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   double age;
-     }
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-     /*  for (i=1;i<=nlstate;i++)
+                            a covariate has 2 modalities */
-         for(j=1;j<=nlstate+ndeath;j++)
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-     fprintf(ficrespow,"\n");
+     if(mobilav==1) mobilavrange=5; /* default */
+     else mobilavrange=mobilav;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     for (age=bage; age<=fage; age++)
-     fclose(ficrespow);
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
-     for(i=1; i <=NDIM; i++)
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-       for(j=i+1;j<=NDIM;j++)
+        we use a 5 terms etc. until the borders are no more concerned.
-         matcov[i][j]=matcov[j][i];
+     */
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-     printf("\nCovariance matrix\n ");
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-     for(i=1; i <=NDIM; i++) {
+         for (i=1; i<=nlstate;i++){
-       for(j=1;j<=NDIM;j++){
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-         printf("%f ",matcov[i][j]);
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-       }
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-       printf("\n ");
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-     }
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+               }
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-     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]));
+         }
+       }/* end age */
-     lsurv=vector(1,AGESUP);
+     }/* end mob */
-     lpop=vector(1,AGESUP);
+   }else return -1;
-     tpop=vector(1,AGESUP);
+   return 0;
-     lsurv[agegomp]=100000;
+ }/* End movingaverage */
-     for (k=agegomp;k<=AGESUP;k++) {
-       agemortsup=k;
+ /************** Forecasting ******************/
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+ void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
-     }
+   /* proj1, year, month, day of starting projection
+      agemin, agemax range of age
-     for (k=agegomp;k<agemortsup;k++)
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+      anproj2 year of en of projection (same day and month as proj1).
+   */
-     for (k=agegomp;k<agemortsup;k++){
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   double agec; /* generic age */
-       sumlpop=sumlpop+lpop[k];
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-     }
+   double *popeffectif,*popcount;
+   double ***p3mat;
-     tpop[agegomp]=sumlpop;
+   double ***mobaverage;
-     for (k=agegomp;k<(agemortsup-3);k++){
+   char fileresf[FILENAMELENGTH];
-       /*  tpop[k+1]=2;*/
-       tpop[k+1]=tpop[k]-lpop[k];
+   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.
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   */
-     for (k=agegomp;k<(agemortsup-2);k++)
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
-       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]);
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   strcpy(fileresf,"F_");
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   strcat(fileresf,fileresu);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-                      stepm, weightopt,\
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-                      model,imx,p,matcov,agemortsup);
+   }
+   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
-     free_vector(lsurv,1,AGESUP);
+   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
-     free_vector(lpop,1,AGESUP);
-     free_vector(tpop,1,AGESUP);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   } /* Endof if mle==-3 */
+   if (mobilav!=0) {
-   else{ /* For mle >=1 */
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     for (k=1; k<=npar;k++)
+     }
-       printf(" %d %8.5f",k,p[k]);
+   }
-     printf("\n");
-     globpr=1; /* to print the contributions */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   if (stepm<=12) stepsize=1;
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   if(estepm < stepm){
-     for (k=1; k<=npar;k++)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       printf(" %d %8.5f",k,p[k]);
+   }
-     printf("\n");
+   else  hstepm=estepm;
-     if(mle>=1){ /* Could be 1 or 2 */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+   hstepm=hstepm/stepm;
-     }
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
-     /*--------- results files --------------*/
+   anprojmean=yp;
-     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);
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   jprojmean=yp;
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   if(jprojmean==0) jprojmean=1;
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   if(mprojmean==0) jprojmean=1;
-     for(i=1,jk=1; i <=nlstate; i++){
-       for(k=1; k <=(nlstate+ndeath); k++){
+   i1=cptcoveff;
-         if (k != i) {
+   if (cptcovn < 1){i1=1;}
-           printf("%d%d ",i,k);
-           fprintf(ficlog,"%d%d ",i,k);
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-           fprintf(ficres,"%1d%1d ",i,k);
-           for(j=1; j <=ncovmodel; j++){
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+ /*            if (h==(int)(YEARM*yearp)){ */
-             fprintf(ficres,"%lf ",p[jk]);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-             jk++;
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-           }
+       k=k+1;
-           printf("\n");
+       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-           fprintf(ficlog,"\n");
+       for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficres,"\n");
+         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         }
+       }
-       }
+       fprintf(ficresf," yearproj age");
-     }
+       for(j=1; j<=nlstate+ndeath;j++){
-     if(mle!=0){
+         for(i=1; i<=nlstate;i++)
-       /* Computing hessian and covariance matrix */
+           fprintf(ficresf," p%d%d",i,j);
-       ftolhess=ftol; /* Usually correct */
+         fprintf(ficresf," p.%d",j);
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+       }
-     }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+         fprintf(ficresf,"\n");
-     printf("# Scales (for hessian or gradient estimation)\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-     for(i=1,jk=1; i <=nlstate; i++){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-       for(j=1; j <=nlstate+ndeath; j++){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-         if (j!=i) {
+           nhstepm = nhstepm/hstepm;
-           fprintf(ficres,"%1d%1d",i,j);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           printf("%1d%1d",i,j);
+           oldm=oldms;savm=savms;
-           fprintf(ficlog,"%1d%1d",i,j);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-           for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
+           for (h=0; h<=nhstepm; h++){
-             fprintf(ficlog," %.5e",delti[jk]);
+             if (h*hstepm/YEARM*stepm ==yearp) {
-             fprintf(ficres," %.5e",delti[jk]);
+               fprintf(ficresf,"\n");
-             jk++;
+               for(j=1;j<=cptcoveff;j++)
-           }
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-           printf("\n");
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-           fprintf(ficlog,"\n");
+             }
-           fprintf(ficres,"\n");
+             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];
-     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");
+                 else {
-     if(mle>=1)
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-       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");
+                 if (h*hstepm/YEARM*stepm== yearp) {
-     /* # 121 Var(a12)\n\ */
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                 }
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+               } /* end i */
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+               if (h*hstepm/YEARM*stepm==yearp) {
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                 fprintf(ficresf," %.3f", ppij);
-     /* # 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\ */
+             }/* end j */
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+           } /* end h */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         } /* end agec */
-     /* Just to have a covariance matrix which will be more understandable
+       } /* end yearp */
-        even is we still don't want to manage dictionary of variables
+     } /* end cptcod */
-     */
+   } /* end  cptcov */
-     for(itimes=1;itimes<=2;itimes++){
-       jj=0;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       for(i=1; i <=nlstate; i++){
-         for(j=1; j <=nlstate+ndeath; j++){
+   fclose(ficresf);
-           if(j==i) continue;
+   printf("End of Computing forecasting \n");
-           for(k=1; k<=ncovmodel;k++){
+   fprintf(ficlog,"End of Computing forecasting\n");
-             jj++;
-             ca[0]= k+'a'-1;ca[1]='\0';
+ }
-             if(itimes==1){
-               if(mle>=1)
+ /************** Forecasting *****not tested NB*************/
-                 printf("#%1d%1d%d",i,j,k);
+ 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){
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-             }else{
+   int *popage;
-               if(mle>=1)
+   double calagedatem, agelim, kk1, kk2;
-                 printf("%1d%1d%d",i,j,k);
+   double *popeffectif,*popcount;
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+   double ***p3mat,***tabpop,***tabpopprev;
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+   double ***mobaverage;
-             }
+   char filerespop[FILENAMELENGTH];
-             ll=0;
-             for(li=1;li <=nlstate; li++){
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                 if(lj==li) continue;
+   agelim=AGESUP;
-                 for(lk=1;lk<=ncovmodel;lk++){
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-                   ll++;
-                   if(ll<=jj){
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-                     cb[0]= lk +'a'-1;cb[1]='\0';
-                     if(ll<jj){
-                       if(itimes==1){
+   strcpy(filerespop,"POP_");
-                         if(mle>=1)
+   strcat(filerespop,fileresu);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-                       }else{
+   }
-                         if(mle>=1)
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-                           printf(" %.5e",matcov[jj][ll]);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-                       }
-                     }else{
+   if (mobilav!=0) {
-                       if(itimes==1){
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                         if(mle>=1)
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     }
-                       }else{
+   }
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   if (stepm<=12) stepsize=1;
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+   agelim=AGESUP;
-                     }
-                   }
+   hstepm=1;
-                 } /* end lk */
+   hstepm=hstepm/stepm;
-               } /* end lj */
-             } /* end li */
+   if (popforecast==1) {
-             if(mle>=1)
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-               printf("\n");
+       printf("Problem with population file : %s\n",popfile);exit(0);
-             fprintf(ficlog,"\n");
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-             fprintf(ficres,"\n");
+     }
-             numlinepar++;
+     popage=ivector(0,AGESUP);
-           } /* end k*/
+     popeffectif=vector(0,AGESUP);
-         } /*end j */
+     popcount=vector(0,AGESUP);
-       } /* end i */
-     } /* end itimes */
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-     fflush(ficlog);
-     fflush(ficres);
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   }
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-       puts(line);
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       fputs(line,ficparo);
+       k=k+1;
-     }
+       fprintf(ficrespop,"\n#******");
-     ungetc(c,ficpar);
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     estepm=0;
+       }
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+       fprintf(ficrespop,"******\n");
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+       fprintf(ficrespop,"# Age");
-     if (fage <= 2) {
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-       bage = ageminpar;
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-       fage = agemaxpar;
-     }
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fgets(line, MAXLINE, ficpar);
+           oldm=oldms;savm=savms;
-       puts(line);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-       fputs(line,ficparo);
-     }
+           for (h=0; h<=nhstepm; h++){
-     ungetc(c,ficpar);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     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);
+             for(j=1; j<=nlstate+ndeath;j++) {
-     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);
+               kk1=0.;kk2=0;
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+               for(i=1; i<=nlstate;i++) {
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+                 else {
-       ungetc(c,ficpar);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-       fgets(line, MAXLINE, ficpar);
+                 }
-       puts(line);
+               }
-       fputs(line,ficparo);
+               if (h==(int)(calagedatem+12*cpt)){
-     }
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-     ungetc(c,ficpar);
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+             }
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+                 for(j=1; j<=nlstate;j++){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-     fprintf(ficres,"pop_based=%d\n",popbased);
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+             }
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-       puts(line);
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-       fputs(line,ficparo);
+           }
-     }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     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);
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-     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(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     /* day and month of proj2 are not used but only year anproj2.*/
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+           for (h=0; h<=nhstepm; h++){
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+             }
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+             for(j=1; j<=nlstate+ndeath;j++) {
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
-    /*------------ free_vector  -------------*/
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-    /*  chdir(path); */
+               }
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-     free_ivector(wav,1,imx);
+             }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+           }
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,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);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     fclose(ficres);
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     free_vector(popeffectif,0,AGESUP);
+     free_vector(popcount,0,AGESUP);
-     strcpy(filerespl,"pl");
+   }
-     strcat(filerespl,fileres);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   fclose(ficrespop);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+ } /* End of popforecast */
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ int fileappend(FILE *fichier, char *optionfich)
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ {
-     pstamp(ficrespl);
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     printf("Problem with file: %s\n", optionfich);
-     fprintf(ficrespl,"#Age ");
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     return (0);
-     fprintf(ficrespl,"\n");
+   }
+   fflush(fichier);
-     prlim=matrix(1,nlstate,1,nlstate);
+   return (1);
+ }
-     agebase=ageminpar;
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
+ /**************** function prwizard **********************/
-     i1=cptcoveff;
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-     if (cptcovn < 1){i1=1;}
+ {
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   /* Wizard to print covariance matrix template */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+   char ca[32], cb[32];
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-         fprintf(ficrespl,"\n#******");
+   int numlinepar;
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-         for(j=1;j<=cptcoveff;j++) {
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   for(i=1; i <=nlstate; i++){
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     jj=0;
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(j=1; j <=nlstate+ndeath; j++){
-         }
+       if(j==i) continue;
-         fprintf(ficrespl,"******\n");
+       jj++;
-         printf("******\n");
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-         fprintf(ficlog,"******\n");
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
-         for (age=agebase; age<=agelim; age++){
+       for(k=1; k<=ncovmodel;k++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         /*        printf(" %lf",param[i][j][k]); */
-           fprintf(ficrespl,"%.0f ",age );
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-           for(j=1;j<=cptcoveff;j++)
+         printf(" 0.");
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficparo," 0.");
-           for(i=1; i<=nlstate;i++)
+       }
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       printf("\n");
-           fprintf(ficrespl,"\n");
+       fprintf(ficparo,"\n");
-         }
+     }
-       }
+   }
-     }
+   printf("# Scales (for hessian or gradient estimation)\n");
-     fclose(ficrespl);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     /*------------- h Pij x at various ages ------------*/
+   for(i=1; i <=nlstate; i++){
+     jj=0;
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     for(j=1; j <=nlstate+ndeath; j++){
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       if(j==i) continue;
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       jj++;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficparo,"%1d%1d",i,j);
-     }
+       printf("%1d%1d",i,j);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+       fflush(stdout);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-     /*if (stepm<=24) stepsize=2;*/
+         printf(" 0.");
+         fprintf(ficparo," 0.");
-     agelim=AGESUP;
+       }
-     hstepm=stepsize*YEARM; /* Every year of age */
+       numlinepar++;
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+       printf("\n");
+       fprintf(ficparo,"\n");
-     /* 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 ");
+   printf("# Covariance matrix\n");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ /* # 121 Var(a12)\n\ */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-         k=k+1;
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         fprintf(ficrespij,"\n#****** ");
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         for(j=1;j<=cptcoveff;j++)
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-         fprintf(ficrespij,"******\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" */
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+   fflush(stdout);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   fprintf(ficparo,"# Covariance matrix\n");
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+   for(itimes=1;itimes<=2;itimes++){
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     jj=0;
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     for(i=1; i <=nlstate; i++){
-           for(i=1; i<=nlstate;i++)
+       for(j=1; j <=nlstate+ndeath; j++){
-             for(j=1; j<=nlstate+ndeath;j++)
+         if(j==i) continue;
-               fprintf(ficrespij," %1d-%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
-           fprintf(ficrespij,"\n");
+           jj++;
-           for (h=0; h<=nhstepm; h++){
+           ca[0]= k+'a'-1;ca[1]='\0';
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+           if(itimes==1){
-             for(i=1; i<=nlstate;i++)
+             printf("#%1d%1d%d",i,j,k);
-               for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           }else{
-             fprintf(ficrespij,"\n");
+             printf("%1d%1d%d",i,j,k);
-           }
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             /*  printf(" %.5le",matcov[i][j]); */
-           fprintf(ficrespij,"\n");
+           }
-         }
+           ll=0;
-       }
+           for(li=1;li <=nlstate; li++){
-     }
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
-     fclose(ficrespij);
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                   if(ll<jj){
-     for(i=1;i<=AGESUP;i++)
+                     if(itimes==1){
-       for(j=1;j<=NCOVMAX;j++)
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-         for(k=1;k<=NCOVMAX;k++)
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-           probs[i][j][k]=0.;
+                     }else{
+                       printf(" 0.");
-     /*---------- Forecasting ------------------*/
+                       fprintf(ficparo," 0.");
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+                     }
-     if(prevfcast==1){
+                   }else{
-       /*    if(stepm ==1){*/
+                     if(itimes==1){
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-       /*      }  */
+                     }else{
-       /*      else{ */
+                       printf(" 0.");
-       /*        erreur=108; */
+                       fprintf(ficparo," 0.");
-       /*        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); */
+                   }
-       /*      } */
+                 }
-     }
+               } /* end lk */
+             } /* end lj */
+           } /* end li */
-     /*---------- Health expectancies and variances ------------*/
+           printf("\n");
+           fprintf(ficparo,"\n");
-     strcpy(filerest,"t");
+           numlinepar++;
-     strcat(filerest,fileres);
+         } /* end k*/
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+       } /*end j */
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     } /* end i */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   } /* end itimes */
-     }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+ } /* end of prwizard */
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
-     strcpy(filerese,"e");
+   double A,B,L=0.0,sump=0.,num=0.;
-     strcat(filerese,fileres);
+   int i,n=0; /* n is the size of the sample */
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   for (i=0;i<=imx-1 ; i++) {
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     sump=sump+weight[i];
-     }
+     /*    sump=sump+1;*/
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     num=num+1;
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   }
-     strcpy(fileresstde,"stde");
-     strcat(fileresstde,fileres);
+   /* for (i=0; i<=imx; i++)
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+      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("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);
+   for (i=1;i<=imx ; i++)
-     }
+     {
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+       if (cens[i] == 1 && wav[i]>1)
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-     strcpy(filerescve,"cve");
+       if (cens[i] == 0 && wav[i]>1)
-     strcat(filerescve,fileres);
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-       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);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     }
+       if (wav[i] > 1 ) { /* ??? */
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+         L=L+A*weight[i];
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+         /*      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]);*/
+       }
-     strcpy(fileresv,"v");
+     }
-     strcat(fileresv,fileres);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+   return -2*L*num/sump;
-     }
+ }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+ double gompertz_f(const gsl_vector *v, void *params)
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ {
-     /*  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",\
+   double A,B,LL=0.0,sump=0.,num=0.;
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+   double *x= (double *) v->data;
-     */
+   int i,n=0; /* n is the size of the sample */
-     if (mobilav!=0) {
+   for (i=0;i<=imx-1 ; i++) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     sump=sump+weight[i];
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     /*    sump=sump+1;*/
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     num=num+1;
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   }
-       }
-     }
+   /* for (i=0; i<=imx; i++)
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      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(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-         k=k+1;
+   for (i=1;i<=imx ; i++)
-         fprintf(ficrest,"\n#****** ");
+     {
-         for(j=1;j<=cptcoveff;j++)
+       if (cens[i] == 1 && wav[i]>1)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-         fprintf(ficrest,"******\n");
+       if (cens[i] == 0 && wav[i]>1)
-         fprintf(ficreseij,"\n#****** ");
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-         fprintf(ficresstdeij,"\n#****** ");
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-         fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       if (wav[i] > 1 ) { /* ??? */
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         LL=LL+A*weight[i];
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         /*      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]);*/
-         }
+       }
-         fprintf(ficreseij,"******\n");
+     }
-         fprintf(ficresstdeij,"******\n");
-         fprintf(ficrescveij,"******\n");
+  /*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);
-         fprintf(ficresvij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+   return -2*LL*num/sump;
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
-         fprintf(ficresvij,"******\n");
+ #endif
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ /******************* Printing html file ***********/
-         oldm=oldms;savm=savms;
+ void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+                   int lastpass, int stepm, int weightopt, char model[],\
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-         if(popbased==1){
+   for (i=1;i<=2;i++)
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+     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>");
-         pstamp(ficrest);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-         fprintf(ficrest,"\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>");
-         epj=vector(1,nlstate+1);
+  for (k=agegomp;k<(agemortsup-2);k++)
-         for(age=bage; age <=fage ;age++){
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           if (popbased==1) {
-             if(mobilav ==0){
+   fflush(fichtm);
-               for(i=1; i<=nlstate;i++)
+ }
-                 prlim[i][i]=probs[(int)age][i][k];
-             }else{ /* mobilav */
+ /******************* Gnuplot file **************/
-               for(i=1; i<=nlstate;i++)
+ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-                 prlim[i][i]=mobaverage[(int)age][i][k];
-             }
+   char dirfileres[132],optfileres[132];
-           }
+   int ng;
-           fprintf(ficrest," %4.0f",age);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   /*#ifdef windows */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     /*#endif */
-             }
-             epj[nlstate+1] +=epj[j];
-           }
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   fprintf(ficgp,"set out \"graphmort.svg\"\n ");
-             for(j=1;j <=nlstate;j++)
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-               vepp += vareij[i][j][(int)age];
+   fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-           for(j=1;j <=nlstate;j++){
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-           }
+ }
-           fprintf(ficrest,"\n");
-         }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-         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);
+   /*-------- data file ----------*/
-       }
+   FILE *fic;
-     }
+   char dummy[]="                         ";
-     free_vector(weight,1,n);
+   int i=0, j=0, n=0;
-     free_imatrix(Tvard,1,15,1,2);
+   int linei, month, year,iout;
-     free_imatrix(s,1,maxwav+1,1,n);
+   char line[MAXLINE], linetmp[MAXLINE];
-     free_matrix(anint,1,maxwav,1,n);
+   char stra[MAXLINE], strb[MAXLINE];
-     free_matrix(mint,1,maxwav,1,n);
+   char *stratrunc;
-     free_ivector(cod,1,n);
+   int lstra;
-     free_ivector(tab,1,NCOVMAX);
-     fclose(ficreseij);
-     fclose(ficresstdeij);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     fclose(ficrescveij);
+     printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
-     fclose(ficresvij);
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
-     fclose(ficrest);
+   }
-     fclose(ficpar);
+   i=1;
-     /*------- Variance of period (stable) prevalence------*/
+   linei=0;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     strcpy(fileresvpl,"vpl");
+     linei=linei+1;
-     strcat(fileresvpl,fileres);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       if(line[j] == '\t')
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+         line[j] = ' ';
-       exit(0);
+     }
-     }
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+       ;
+     };
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     line[j+1]=0;  /* Trims blanks at end of line */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     if(line[0]=='#'){
-         k=k+1;
+       fprintf(ficlog,"Comment line\n%s\n",line);
-         fprintf(ficresvpl,"\n#****** ");
+       printf("Comment line\n%s\n",line);
-         for(j=1;j<=cptcoveff;j++)
+       continue;
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     }
-         fprintf(ficresvpl,"******\n");
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     strcpy(line, linetmp);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     for (j=maxwav;j>=1;j--){
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       cutv(stra, strb, line, ' ');
-       }
+       if(strb[0]=='.') { /* Missing status */
-     }
+         lval=-1;
+       }else{
-     fclose(ficresvpl);
+         errno=0;
+         lval=strtol(strb,&endptr,10);
-     /*---------- End : free ----------------*/
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           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);
-   }  /* mle==-3 arrives here for freeing */
+           return 1;
-   free_matrix(prlim,1,nlstate,1,nlstate);
+         }
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+       }
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       s[j][i]=lval;
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       strcpy(line,stra);
-     free_matrix(covar,0,NCOVMAX,1,n);
+       cutv(stra, strb,line,' ');
-     free_matrix(matcov,1,npar,1,npar);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-     /*free_vector(delti,1,npar);*/
+       }
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-     free_matrix(agev,1,maxwav,1,imx);
+         month=99;
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         year=9999;
+       }else{
-     free_ivector(ncodemax,1,8);
+         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);
-     free_ivector(Tvar,1,15);
+         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);
-     free_ivector(Tprod,1,15);
+         return 1;
-     free_ivector(Tvaraff,1,15);
+       }
-     free_ivector(Tage,1,15);
+       anint[j][i]= (double) year;
-     free_ivector(Tcode,1,100);
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     } /* ENd Waves */
-     free_imatrix(codtab,1,100,1,10);
-   fflush(fichtm);
+     cutv(stra, strb,line,' ');
-   fflush(ficgp);
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-   if((nberr >0) || (nbwarn>0)){
+       month=99;
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+       year=9999;
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     }else{
-   }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);
-     printf("End of Imach\n");
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     fprintf(ficlog,"End of Imach\n");
+         return 1;
-   }
+     }
-   printf("See log file on %s\n",filelog);
+     andc[i]=(double) year;
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     moisdc[i]=(double) month;
-   (void) gettimeofday(&end_time,&tzp);
+     strcpy(line,stra);
-   tm = *localtime(&end_time.tv_sec);
-   tmg = *gmtime(&end_time.tv_sec);
+     cutv(stra, strb,line,' ');
-   strcpy(strtend,asctime(&tm));
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-   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);
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+       month=99;
+       year=9999;
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     }else{
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+       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,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+       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);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+         return 1;
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     }
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     if (year==9999) {
-   fclose(fichtm);
+       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(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+       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);
-   fclose(fichtmcov);
+         return 1;
-   fclose(ficgp);
-   fclose(ficlog);
+     }
-   /*------ End -----------*/
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
-    printf("Before Current directory %s!\n",pathcd);
-    if(chdir(pathcd) != 0)
+     cutv(stra, strb,line,' ');
-     printf("Can't move to directory %s!\n",path);
+     errno=0;
-   if(getcwd(pathcd,MAXLINE) > 0)
+     dval=strtod(strb,&endptr);
-     printf("Current directory %s!\n",pathcd);
+     if( strb[0]=='\0' || (*endptr != '\0')){
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-   sprintf(plotcmd,"gnuplot");
+       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);
- #ifndef UNIX
+       fflush(ficlog);
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+       return 1;
- #endif
+     }
-   if(!stat(plotcmd,&info)){
+     weight[i]=dval;
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     strcpy(line,stra);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     for (j=ncovcol;j>=1;j--){
-     }else
+       cutv(stra, strb,line,' ');
-       strcpy(pplotcmd,plotcmd);
+       if(strb[0]=='.') { /* Missing status */
- #ifdef UNIX
+         lval=-1;
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+       }else{
-     if(!stat(plotcmd,&info)){
+         errno=0;
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+         lval=strtol(strb,&endptr,10);
-     }else
+         if( strb[0]=='\0' || (*endptr != '\0')){
-       strcpy(pplotcmd,plotcmd);
+           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);
- #endif
+           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);
-   }else
+           return 1;
-     strcpy(pplotcmd,plotcmd);
+         }
+       }
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+       if(lval <-1 || lval >1){
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+         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 \
-   if((outcmd=system(plotcmd)) != 0){
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     printf("\n Problem with gnuplot\n");
+  For example, for multinomial values like 1, 2 and 3,\n \
-   }
+  build V1=0 V2=0 for the reference value (1),\n \
-   printf(" Wait...");
+         V1=1 V2=0 for (2) \n \
-   while (z[0] != 'q') {
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     /* chdir(path); */
+  output of IMaCh is often meaningless.\n \
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+  Exiting.\n",lval,linei, i,line,j);
-     scanf("%s",z);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
- /*     if (z[0] == 'c') system("./imach"); */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     if (z[0] == 'e') {
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+  For example, for multinomial values like 1, 2 and 3,\n \
-       system(optionfilehtm);
+  build V1=0 V2=0 for the reference value (1),\n \
-     }
+         V1=1 V2=0 for (2) \n \
-     else if (z[0] == 'g') system(plotcmd);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     else if (z[0] == 'q') exit(0);
+  output of IMaCh is often meaningless.\n \
-   }
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-   end:
+         return 1;
-   while (z[0] != 'q') {
+       }
-     printf("\nType  q for exiting: ");
+       covar[j][i]=(double)(lval);
-     scanf("%s",z);
+       strcpy(line,stra);
-   }
+     }
- }
+     lstra=strlen(stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
+       num[i]=atol(stratrunc);
+     }
+     else
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     i=i+1;
+   } /* End loop reading  data */
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
+   return (0);
+   /* endread: */
+     printf("Exiting readdata: ");
+     fclose(fic);
+     return (1);
+ }
+ void removespace(char *str) {
+   char *p1 = str, *p2 = str;
+   do
+     while (*p2 == ' ')
+       p2++;
+   while (*p1++ == *p2++);
+ }
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+    * - nagesqr = 1 if age*age in the model, otherwise 0.
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
+    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+    * - cptcovage number of covariates with age*products =2
+    * - cptcovs number of simple covariates
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+    *     which is a new column after the 9 (ncovcol) variables.
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+  */
+ {
+   int i, j, k, ks;
+   int  j1, k1, k2;
+   char modelsav[80];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char *strpt;
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     if (strstr(model,"AGE") !=0){
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
+       return 1;
+     }
+     if (strstr(model,"v") !=0){
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
+     }
+     strcpy(modelsav,model);
+     if ((strpt=strstr(model,"age*age")) !=0){
+       printf(" strpt=%s, model=%s\n",strpt, model);
+       if(strpt != model){
+       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+  corresponding column of parameters.\n",model);
+       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+  corresponding column of parameters.\n",model); fflush(ficlog);
+       return 1;
+     }
+       nagesqr=1;
+       if (strstr(model,"+age*age") !=0)
+         substrchaine(modelsav, model, "+age*age");
+       else if (strstr(model,"age*age+") !=0)
+         substrchaine(modelsav, model, "age*age+");
+       else
+         substrchaine(modelsav, model, "age*age");
+     }else
+       nagesqr=0;
+     if (strlen(modelsav) >1){
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
+       cptcovt= j+1; /* Number of total covariates in the model, not including
+                    * cst, age and age*age
+                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
+                   /* including age products which are counted in cptcovage.
+                   * but the covariates which are products must be treated
+                   * separately: ncovn=4- 2=2 (V1+V3). */
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+       /*   Design
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+        *  <          ncovcol=8                >
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+        *   k=  1    2      3       4     5       6      7        8
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+        *  covar[k,i], value of kth covariate if not including age for individual i:
+        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+        *  Tage[++cptcovage]=k
+        *       if products, new covar are created after ncovcol with k1
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+        *  <          ncovcol=8                >
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tprod[1]@2={                         6, 5}
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+        *How to reorganize?
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
+        * Struct []
+        */
+       /* This loop fills the array Tvar from the string 'model'.*/
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
+       /*        k=1 Tvar[1]=2 (from V2) */
+       /*        k=5 Tvar[5] */
+       /* for (k=1; k<=cptcovn;k++) { */
+       /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       /*        } */
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
+       /*
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
+       cptcovage=0;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*scanf("%d",i);*/
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+             /* covar is not filled and then is empty */
+             cptcovprod--;
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             /*printf("stre=%s ", stre);*/
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+             cptcovprod--;
+             cutl(stre,strb,strc,'V');
+             Tvar[k]=atoi(stre);
+             cptcovage++;
+             Tage[cptcovage]=k;
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             cptcovn++;
+             cptcovprodnoage++;k1++;
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+                                    because this model-covariate is a construction we invent a new column
+                                    ncovcol + k1
+                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             k2=k2+2;
+             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+             for (i=1; i<=lastobs;i++){
+               /* Computes the new covariate which is a product of
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+             }
+           } /* End age is not in the model */
+         } /* End if model includes a product */
+         else { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates */
+           cptcovn++;
+           Tvar[k]=atoi(strd);
+         }
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+           scanf("%d",i);*/
+       } /* end of loop + on total covariates */
+     } /* end if strlen(modelsave == 0) age*age might exist */
+   } /* end if strlen(model == 0) */
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   scanf("%d ",i);*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
+   /*endread:*/
+     printf("Exiting decodemodel: ");
+     return (1);
+ }
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
+   int i, m;
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         *nberr = *nberr + 1;
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+         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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         (*nberr)++;
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
+     }
+   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
+       if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
+         if (s[m][i] >= nlstate+1) {
+           if(agedc[i]>0){
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
+               agev[m][i]=agedc[i];
+               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             }else {
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 agev[m][i]=-1;
+               }
+             }
+           } /* agedc > 0 */
+         } /* end if */
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
+           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
+         } /* en if 9*/
+         else { /* =9 */
+           /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
+           agev[m][i]=1;
+           s[m][i]=-1;
+         }
+       }
+       else if(s[m][i]==0) /*= 0 Unknown */
+         agev[m][i]=1;
+       else{
+         printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         agev[m][i]=0;
+       }
+     } /* End for lastpass */
+   }
+   for (i=1; i<=imx; i++)  {
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
+         (*nberr)++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 1;
+       }
+     }
+   }
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
+ }*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   return (0);
+  /* endread:*/
+     printf("Exiting calandcheckages: ");
+     return (1);
+ }
+ #if defined(_MSC_VER)
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ //#include "stdafx.h"
+ //#include <stdio.h>
+ //#include <tchar.h>
+ //#include <windows.h>
+ //#include <iostream>
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
+ BOOL IsWow64()
+ {
+         BOOL bIsWow64 = FALSE;
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
+         //  (HANDLE, PBOOL);
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
+         HMODULE module = GetModuleHandle(_T("kernel32"));
+         const char funcName[] = "IsWow64Process";
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
+                 GetProcAddress(module, funcName);
+         if (NULL != fnIsWow64Process)
+         {
+                 if (!fnIsWow64Process(GetCurrentProcess(),
+                         &bIsWow64))
+                         //throw std::exception("Unknown error");
+                         printf("Unknown error\n");
+         }
+         return bIsWow64 != FALSE;
+ }
+ #endif
+ void syscompilerinfo(int logged)
+  {
+    /* #include "syscompilerinfo.h"*/
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
+ #endif
+ #include <stdint.h>
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+ #endif
+ #if defined(_MSC_VER)
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+ #endif
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
+    printf(" for "); if (logged) fprintf(ficlog, " for ");
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
+     // Windows (x64 and x86)
+    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
+ #elif __unix__ // all unices, not all compilers
+     // Unix
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
+ #elif __linux__
+     // linux
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
+ #elif __APPLE__
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
+ #endif
+ /*  __MINGW32__   */
+ /*  __CYGWIN__   */
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
+ /* _WIN64  // Defined for applications for Win64. */
+ /* _M_X64 // Defined for compilations that target x64 processors. */
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
+ #if UINTPTR_MAX == 0xffffffff
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
+ #endif
+ #if defined(__GNUC__)
+ # if defined(__GNUC_PATCHLEVEL__)
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100)
+ # endif
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+    if (uname(&sysInfo) != -1) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+ #endif
+    //   void main()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+  }
+  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   int i, j, k, i1 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(filerespl,"PL_");
+   strcat(filerespl,fileresu);
+   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   fprintf(ficrespl,"\n");
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+     agebase=ageminpar;
+     agelim=agemaxpar;
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         /* to clean */
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+         fprintf(ficrespl,"#******");
+         printf("#******");
+         fprintf(ficlog,"#******");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         fprintf(ficrespl,"#Age ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+         fprintf(ficrespl,"Total Years_to_converge\n");
+         for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+           fprintf(ficrespl,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           tot=0.;
+           for(i=1; i<=nlstate;i++){
+             tot +=  prlim[i][i];
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           }
+           fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         } /* Age */
+         /* was end of cptcod */
+     } /* cptcov */
+         return 0;
+ }
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k;
+   double agedeb;
+   double ***p3mat;
+     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     i1= pow(2,cptcoveff);
+    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+    /*   k=k+1;  */
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespij,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
+       /*}*/
+     }
+         return 0;
+ }
+ /***********************************************/
+ /**************** 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 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 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 ***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 **ximort;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+   int *dcwave;
+   char z[1]="c";
+   /*char  *strt;*/
+   char strtend[80];
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
+   /*tml = *localtime(&start_time.tm_sec);*/
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
+   getcwd(pathcd, size);
+ #endif
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
+     if(!fgets(pathr,FILENAMELENGTH,stdin)){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+     i=strlen(pathr);
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+     }
+     i=strlen(pathr);
+     if( i==0 ){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
+     }
+   }
+   else{
+     strcpy(pathtot,argv[1]);
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   /*cygwin_split_path(pathtot,path,optionfile);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #ifdef WIN32
+   _chdir(path); /* Can be a relative path */
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ #else
+   chdir(path); /* Can be a relative path */
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
+ #endif
+   printf("Current directory %s!\n",pathcd);
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
+   /*-------- arguments in the command line --------*/
+   /* Main Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   syscompilerinfo(1);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
+   /* */
+   strcpy(fileres,"r");
+   strcat(fileres, optionfilefiname);
+   strcat(fileresu, optionfilefiname); /* Without r in front */
+   strcat(fileres,".txt");    /* Other files have txt extension */
+   strcat(fileresu,".txt");    /* Other files have txt extension */
+   /* Main ---------arguments file --------*/
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fflush(ficlog);
+     /* goto end; */
+     exit(70);
+   }
+   strcpy(filereso,"o");
+   strcat(filereso,fileresu);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
+     goto end;
+   }
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
+     /* First parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+     if (num_filled != 5) {
+       printf("Should be 5 parameters\n");
+     }
+     numlinepar++;
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+   }
+   /* Second parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+     if (num_filled != 8) {
+       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       printf("but line=%s\n",line);
+     }
+     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+   /* Third parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled == 0)
+             model[0]='\0';
+     else if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     }
+     else{
+       if (model[0]=='+'){
+         for(i=1; i<=strlen(model);i++)
+           modeltemp[i-1]=model[i];
+         strcpy(model,modeltemp);
+       }
+     }
+     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     printf("model=1+age+%s\n",model);fflush(stdout);
+   }
+   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+   /* numlinepar=numlinepar+3; /\* In general *\/ */
+   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fflush(ficlog);
+   /* if(model[0]=='#'|| model[0]== '\0'){ */
+   if(model[0]=='#'){
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+     if(mle != -1){
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       exit(1);
+     }
+   }
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
+     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+       z[0]=line[1];
+     }
+     /* printf("****line [1] = %c \n",line[1]); */
+     fputs(line, stdout);
+     //puts(line);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
+   */
+   if (strlen(model)>1)
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
+   else
+     ncovmodel=2; /* Constant and age */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
+     fclose (ficlog);
+     goto end;
+     exit(0);
+   }
+   else if(mle==-3) { /* 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{
+     /* 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);
+   agedc=vector(1,n);
+   cod=ivector(1,n);
+   weight=vector(1,n);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   mint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
+     goto end;
+   /* Calculation of the number of parameters from char model */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
+ /* Main decodemodel */
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   /* free_vector(moisdc,1,n); */
+   /* free_vector(andc,1,n); */
+   /* */
+   wav=ivector(1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
+   bh=imatrix(1,lastpass-firstpass+2,1,imx);
+   mw=imatrix(1,lastpass-firstpass+2,1,imx);
+   /* Concatenates waves */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+      Death is a valid wave (if date is known).
+      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+      and mw[mi+1][i]. dh depends on stepm.
+   */
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   ncodemax[1]=1;
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   /* 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)= 00000001 >> (2-1) = 1 right shift
+      *           &
+      *     1        00000001 (1)
+      *              00000001        = 1 & ((h-1) >> (k-1))
+      *          +1= 00000010 =2
+      *
+      * 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
+      */
+   /* /\* for(h=1; h <=100 ;h++){  *\/ */
+   /*   /\* printf("h=%2d ", h); *\/ */
+   /*    /\* for(k=1; k <=10; k++){ *\/ */
+   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
+   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
+   /*    /\* } *\/ */
+   /*    /\* printf("\n"); *\/ */
+   /* } */
+   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
+   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
+   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
+   /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
+   /*      h++; */
+   /*      if (h>m)  */
+   /*        h=1; */
+   /*      codtab[h][k]=j; */
+   /*      /\* codtab[12][3]=1; *\/ */
+   /*      /\*codtab[h][Tvar[k]]=j;*\/ */
+   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
+   /*    }  */
+   /*     } */
+   /*   } */
+   /* }  */
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
+   /* for(i=1; i <=m ;i++){  */
+   /*    for(k=1; k <=cptcovn; k++){ */
+   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
+   /*    } */
+   /*    printf("\n"); */
+   /* } */
+   /*   scanf("%d",i);*/
+  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 prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,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);
+     /*     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 / */
+     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
+       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);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 mortality only */
+   /* Standard  */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
+     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+       /* mlikeli uses func not funcone */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     }
+     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle != 0){
+       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
+       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     /*  */
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle >= 1) /* To big for the screen */
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.7e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+       while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+     /*   ungetc(c,ficpar); */
+     /*   fgets(line, MAXLINE, ficpar); */
+     /*   fputs(line,stdout); */
+     /*   fputs(line,ficparo); */
+     /* } */
+     /* ungetc(c,ficpar); */
+     estepm=0;
+     if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
+     if (num_filled != 6) {
+       printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
+       printf("but line=%s\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.*/
+      /* 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, pathc,p);
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,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);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* ------ Other prevalence ratios------------ */
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  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",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     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);
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- 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(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     printf("done evsij\n");fflush(stdout);
+     fprintf(ficlog,"done evsij\n");fflush(ficlog);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"T_");
+     strcat(filerest,fileresu);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
+     strcpy(fileresstde,"STDE_");
+     strcat(fileresstde,fileresu);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"CVE_");
+     strcat(filerescve,fileresu);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"V_");
+     strcat(fileresv,fileresu);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
+     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrest,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrest,"******\n");
+       fprintf(ficresstdeij,"\n#****** ");
+       fprintf(ficrescveij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       fprintf(ficresstdeij,"******\n");
+       fprintf(ficrescveij,"******\n");
+       fprintf(ficresvij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresvij,"******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       printf(" cvevsij %d, ",k);
+       fprintf(ficlog, " cvevsij %d, ",k);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       printf(" end cvevsij \n ");
+       fprintf(ficlog, " end cvevsij \n ");
+       /*
+        */
+       /* goto endfree; */
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       pstamp(ficrest);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+         cptcod= 0; /* To be deleted */
+         printf("varevsij %d \n",vpopbased);
+         fprintf(ficlog, "varevsij %d \n",vpopbased);
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+         if(vpopbased==1)
+           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+         else
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+         epj=vector(1,nlstate+1);
+         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           if (vpopbased==1) {
+             if(mobilav ==0){
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
+             }
+           }
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
+           /* printf(" age %4.0f ",age); */
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
+             }
+             epj[nlstate+1] +=epj[j];
+           }
+           /* printf(" age %4.0f \n",age); */
+           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(j=1;j <=nlstate;j++)
+               vepp += vareij[i][j][(int)age];
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           for(j=1;j <=nlstate;j++){
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+           }
+           fprintf(ficrest,"\n");
+         }
+       } /* End vpopbased */
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_vector(epj,1,nlstate+1);
+       printf("done \n");fflush(stdout);
+       fprintf(ficlog,"done\n");fflush(ficlog);
+       /*}*/
+     } /* End k */
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     printf("done Health expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     printf("done variance-covariance of period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     free_matrix(hess,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(ncodemaxwundef,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(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\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\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);
+   }
+ }

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.125
changed lines
	Added in v.1.215