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Diff for /imach/src/imach.c between versions 1.125 and 1.193

-version 1.125, 2006/04/04 15:20:31
+version 1.193, 2015/08/04 07:17:42
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 POWELL /* Instead of NLOPT */
- /* #include <sys/time.h> */
+ #define POWELLF1F3 /* Skip test */
- #include <time.h>
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
- #include "timeval.h"
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
- /* #include <libintl.h> */
+ #include <math.h>
- /* #define _(String) gettext (String) */
+ #include <stdio.h>
+ #include <stdlib.h>
- #define MAXLINE 256
+ #include <string.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #ifdef _WIN32
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <io.h>
- #define FILENAMELENGTH 132
+ #include <windows.h>
+ #include <tchar.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #else
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <unistd.h>
+ #endif
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #include <limits.h>
+ #include <sys/types.h>
- #define NINTERVMAX 8
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #if defined(__GNUC__)
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #endif
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #include <sys/stat.h>
- #define AGESUP 130
+ #include <errno.h>
- #define AGEBASE 40
+ /* extern int errno; */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #ifdef UNIX
+ /* #ifdef LINUX */
- #define DIRSEPARATOR '/'
+ /* #include <time.h> */
- #define CHARSEPARATOR "/"
+ /* #include "timeval.h" */
- #define ODIRSEPARATOR '\\'
+ /* #else */
- #else
+ /* #include <sys/time.h> */
- #define DIRSEPARATOR '\\'
+ /* #endif */
- #define CHARSEPARATOR "\\"
- #define ODIRSEPARATOR '/'
+ #include <time.h>
- #endif
+ #ifdef GSL
- /* $Id$ */
+ #include <gsl/gsl_errno.h>
- /* $State$ */
+ #include <gsl/gsl_multimin.h>
+ #endif
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
- char fullversion[]="$Revision$ $Date$";
- char strstart[80];
+ #ifdef NLOPT
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #include <nlopt.h>
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ typedef struct {
- int nvar;
+   double (* function)(double [] );
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ } myfunc_data ;
- int npar=NPARMAX;
+ #endif
- int nlstate=2; /* Number of live states */
- int ndeath=1; /* Number of dead states */
+ /* #include <libintl.h> */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ /* #define _(String) gettext (String) */
- int popbased=0;
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ #define GNUPLOTPROGRAM "gnuplot"
- int jmin, jmax; /* min, max spacing between 2 waves */
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define FILENAMELENGTH 132
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int mle, weightopt;
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- 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 MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double jmean; /* Mean space between 2 waves */
+ #define NINTERVMAX 8
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- FILE *ficlog, *ficrespow;
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int globpr; /* Global variable for printing or not */
+ #define MAXN 20000
- double fretone; /* Only one call to likelihood */
+ #define YEARM 12. /**< Number of months per year */
- long ipmx; /* Number of contributions */
+ #define AGESUP 130
- double sw; /* Sum of weights */
+ #define AGEBASE 40
- char filerespow[FILENAMELENGTH];
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #ifdef _WIN32
- FILE *ficresilk;
+ #define DIRSEPARATOR '\\'
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define CHARSEPARATOR "\\"
- FILE *ficresprobmorprev;
+ #define ODIRSEPARATOR '/'
- FILE *fichtm, *fichtmcov; /* Html File */
+ #else
- FILE *ficreseij;
+ #define DIRSEPARATOR '/'
- char filerese[FILENAMELENGTH];
+ #define CHARSEPARATOR "/"
- FILE *ficresstdeij;
+ #define ODIRSEPARATOR '\\'
- char fileresstde[FILENAMELENGTH];
+ #endif
- FILE *ficrescveij;
- char filerescve[FILENAMELENGTH];
+ /* $Id$ */
- FILE  *ficresvij;
+ /* $State$ */
- char fileresv[FILENAMELENGTH];
- FILE  *ficresvpl;
+ char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- char fileresvpl[FILENAMELENGTH];
+ char fullversion[]="$Revision$ $Date$";
- char title[MAXLINE];
+ char strstart[80];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- char command[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- int  outcmd=0;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char filerest[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- char fileregp[FILENAMELENGTH];
+ int cptcov=0; /* Working variable */
- char popfile[FILENAMELENGTH];
+ int npar=NPARMAX;
+ int nlstate=2; /* Number of live states */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int ndeath=1; /* Number of dead states */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int popbased=0;
- struct timezone tzp;
- extern int gettimeofday();
+ int *wav; /* Number of waves for this individuual 0 is possible */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int maxwav=0; /* Maxim number of waves */
- long time_value;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- extern long time();
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- char strcurr[80], strfor[80];
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
+                    to the likelihood and the sum of weights (done by funcone)*/
- char *endptr;
+ int mle=1, weightopt=0;
- long lval;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- double dval;
+ 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 NR_END 1
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- #define FREE_ARG char*
+ int countcallfunc=0;  /* Count the number of calls to func */
- #define FTOL 1.0e-10
+ double jmean=1; /* Mean space between 2 waves */
+ double **matprod2(); /* test */
- #define NRANSI
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define ITMAX 200
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ /*FILE *fic ; */ /* Used in readdata only */
- #define TOL 2.0e-4
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficlog, *ficrespow;
- #define CGOLD 0.3819660
+ int globpr=0; /* Global variable for printing or not */
- #define ZEPS 1.0e-10
+ double fretone; /* Only one call to likelihood */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- #define GOLD 1.618034
+ char filerespow[FILENAMELENGTH];
- #define GLIMIT 100.0
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- #define TINY 1.0e-20
+ FILE *ficresilk;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- static double maxarg1,maxarg2;
+ FILE *ficresprobmorprev;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ FILE *fichtm, *fichtmcov; /* Html File */
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ FILE *ficresstdeij;
- #define rint(a) floor(a+0.5)
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
- static double sqrarg;
+ char filerescve[FILENAMELENGTH];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ FILE  *ficresvij;
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char fileresv[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- int imx;
+ char title[MAXLINE];
- int stepm=1;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- /* Stepm, step in month: minimum step interpolation*/
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- int estepm;
+ char command[FILENAMELENGTH];
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ int  outcmd=0;
- int m,nb;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char filelog[FILENAMELENGTH]; /* Log file */
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ char filerest[FILENAMELENGTH];
- double **pmmij, ***probs;
+ char fileregp[FILENAMELENGTH];
- double *ageexmed,*agecens;
+ char popfile[FILENAMELENGTH];
- double dateintmean=0;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- double *weight;
- int **s; /* Status */
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- double *agedc, **covar, idx;
+ /* struct timezone tzp; */
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ /* extern int gettimeofday(); */
- double *lsurv, *lpop, *tpop;
+ struct tm tml, *gmtime(), *localtime();
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ extern time_t time();
- double ftolhess; /* Tolerance for computing hessian */
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- /**************** split *************************/
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ struct tm tm;
- {
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ char strcurr[80], strfor[80];
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ char *endptr;
-   char  *ss;                            /* pointer */
+ long lval;
-   int   l1, l2;                         /* length counters */
+ double dval;
-   l1 = strlen(path );                   /* length of path */
+ #define NR_END 1
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define FREE_ARG char*
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define FTOL 1.0e-10
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ #define NRANSI
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ #define ITMAX 200
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-     /* get current working directory */
+ #define TOL 2.0e-4
-     /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define CGOLD 0.3819660
-       return( GLOCK_ERROR_GETCWD );
+ #define ZEPS 1.0e-10
-     }
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     /* got dirc from getcwd*/
-     printf(" DIRC = %s \n",dirc);
+ #define GOLD 1.618034
-   } else {                              /* strip direcotry from path */
+ #define GLIMIT 100.0
-     ss++;                               /* after this, the filename */
+ #define TINY 1.0e-20
-     l2 = strlen( ss );                  /* length of filename */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ static double maxarg1,maxarg2;
-     strcpy( name, ss );         /* save file name */
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     dirc[l1-l2] = 0;                    /* add zero */
-     printf(" DIRC2 = %s \n",dirc);
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   }
+ #define rint(a) floor(a+0.5)
-   /* We add a separator at the end of dirc if not exists */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-   l1 = strlen( dirc );                  /* length of directory */
+ #define mytinydouble 1.0e-16
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     dirc[l1] =  DIRSEPARATOR;
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-     dirc[l1+1] = 0;
+ /* static double dsqrarg; */
-     printf(" DIRC3 = %s \n",dirc);
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-   }
+ static double sqrarg;
-   ss = strrchr( name, '.' );            /* find last / */
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   if (ss >0){
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     ss++;
+ int agegomp= AGEGOMP;
-     strcpy(ext,ss);                     /* save extension */
-     l1= strlen( name);
+ int imx;
-     l2= strlen(ss)+1;
+ int stepm=1;
-     strncpy( finame, name, l1-l2);
+ /* Stepm, step in month: minimum step interpolation*/
-     finame[l1-l2]= 0;
-   }
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-   return( 0 );                          /* we're done */
- }
+ int m,nb;
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *Tage,*cens;
- /******************************************/
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
+                    covariate for which somebody answered excluding
- void replace_back_to_slash(char *s, char*t)
+                    undefined. Usually 2: 0 and 1. */
- {
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
-   int i;
+                              covariate for which somebody answered including
-   int lg=0;
+                              undefined. Usually 3: -1, 0 and 1. */
-   i=0;
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-   lg=strlen(t);
+ double **pmmij, ***probs;
-   for(i=0; i<= lg; i++) {
+ double *ageexmed,*agecens;
-     (s[i] = t[i]);
+ double dateintmean=0;
-     if (t[i]== '\\') s[i]='/';
-   }
+ double *weight;
- }
+ int **s; /* Status */
+ double *agedc;
- int nbocc(char *s, char occ)
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
- {
+                   * covar=matrix(0,NCOVMAX,1,n);
-   int i,j=0;
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
-   int lg=20;
+ double  idx;
-   i=0;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-   lg=strlen(s);
+ int *Ndum; /** Freq of modality (tricode */
-   for(i=0; i<= lg; i++) {
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   if  (s[i] == occ ) j++;
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   }
+ double *lsurv, *lpop, *tpop;
-   return j;
- }
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+ double ftolhess; /**< Tolerance for computing hessian */
- void cutv(char *u,char *v, char*t, char occ)
- {
+ /**************** split *************************/
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ {
-      gives u="abcedf" and v="ghi2j" */
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   int i,lg,j,p=0;
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   i=0;
+   */
-   for(j=0; j<=strlen(t)-1; j++) {
+   char  *ss;                            /* pointer */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+   int   l1=0, l2=0;                             /* length counters */
-   }
+   l1 = strlen(path );                   /* length of path */
-   lg=strlen(t);
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   for(j=0; j<p; j++) {
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-     (u[j] = t[j]);
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   }
+     strcpy( name, path );               /* we got the fullname name because no directory */
-      u[p]='\0';
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-    for(j=0; j<= lg; j++) {
+     /* get current working directory */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   }
+ #ifdef WIN32
- }
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #else
- /********************** nrerror ********************/
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
+ #endif
- void nrerror(char error_text[])
+       return( GLOCK_ERROR_GETCWD );
- {
+     }
-   fprintf(stderr,"ERREUR ...\n");
+     /* got dirc from getcwd*/
-   fprintf(stderr,"%s\n",error_text);
+     printf(" DIRC = %s \n",dirc);
-   exit(EXIT_FAILURE);
+   } else {                              /* strip direcotry from path */
- }
+     ss++;                               /* after this, the filename */
- /*********************** vector *******************/
+     l2 = strlen( ss );                  /* length of filename */
- double *vector(int nl, int nh)
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
- {
+     strcpy( name, ss );         /* save file name */
-   double *v;
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     dirc[l1-l2] = '\0';                 /* add zero */
-   if (!v) nrerror("allocation failure in vector");
+     printf(" DIRC2 = %s \n",dirc);
-   return v-nl+NR_END;
+   }
- }
+   /* We add a separator at the end of dirc if not exists */
+   l1 = strlen( dirc );                  /* length of directory */
- /************************ free vector ******************/
+   if( dirc[l1-1] != DIRSEPARATOR ){
- void free_vector(double*v, int nl, int nh)
+     dirc[l1] =  DIRSEPARATOR;
- {
+     dirc[l1+1] = 0;
-   free((FREE_ARG)(v+nl-NR_END));
+     printf(" DIRC3 = %s \n",dirc);
- }
+   }
+   ss = strrchr( name, '.' );            /* find last / */
- /************************ivector *******************************/
+   if (ss >0){
- int *ivector(long nl,long nh)
+     ss++;
- {
+     strcpy(ext,ss);                     /* save extension */
-   int *v;
+     l1= strlen( name);
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+     l2= strlen(ss)+1;
-   if (!v) nrerror("allocation failure in ivector");
+     strncpy( finame, name, l1-l2);
-   return v-nl+NR_END;
+     finame[l1-l2]= 0;
- }
+   }
- /******************free ivector **************************/
+   return( 0 );                          /* we're done */
- void free_ivector(int *v, long nl, long nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ /******************************************/
- /************************lvector *******************************/
+ void replace_back_to_slash(char *s, char*t)
- long *lvector(long nl,long nh)
+ {
- {
+   int i;
-   long *v;
+   int lg=0;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   i=0;
-   if (!v) nrerror("allocation failure in ivector");
+   lg=strlen(t);
-   return v-nl+NR_END;
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- /******************free lvector **************************/
+   }
- void free_lvector(long *v, long nl, long nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
+ char *trimbb(char *out, char *in)
- }
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
- /******************* imatrix *******************************/
+   s=out;
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   while (*in != '\0'){
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- {
+       in++;
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+     }
-   int **m;
+     *out++ = *in++;
+   }
-   /* allocate pointers to rows */
+   *out='\0';
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   return s;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ }
-   m += NR_END;
-   m -= nrl;
+ /* char *substrchaine(char *out, char *in, char *chain) */
+ /* { */
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
-   /* allocate rows and set pointers to them */
+ /*   char *s, *t; */
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ /*   t=in;s=out; */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   while ((*in != *chain) && (*in != '\0')){ */
-   m[nrl] += NR_END;
+ /*     *out++ = *in++; */
-   m[nrl] -= ncl;
+ /*   } */
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ /*   /\* *in matches *chain *\/ */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
-   /* return pointer to array of pointers to rows */
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-   return m;
+ /*   } */
- }
+ /*   in--; chain--; */
+ /*   while ( (*in != '\0')){ */
- /****************** free_imatrix *************************/
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ /*     *out++ = *in++; */
-       int **m;
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-       long nch,ncl,nrh,nrl;
+ /*   } */
-      /* free an int matrix allocated by imatrix() */
+ /*   *out='\0'; */
- {
+ /*   out=s; */
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ /*   return out; */
-   free((FREE_ARG) (m+nrl-NR_END));
+ /* } */
- }
+ char *substrchaine(char *out, char *in, char *chain)
+ {
- /******************* matrix *******************************/
+   /* Substract chain 'chain' from 'in', return and output 'out' */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
- {
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   char *strloc;
-   double **m;
+   strcpy (out, in);
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
-   m += NR_END;
+   if(strloc != NULL){
-   m -= nrl;
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     /* strcpy (strloc, strloc +strlen(chain));*/
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   }
-   m[nrl] += NR_END;
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
-   m[nrl] -= ncl;
+   return out;
+ }
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   return m;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-    */
+ {
- }
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- /*************************free matrix ************************/
+      gives blocc="abcdef" and alocc="ghi2j".
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- {
+   */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   char *s, *t;
-   free((FREE_ARG)(m+nrl-NR_END));
+   t=in;s=in;
- }
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
- /******************* ma3x *******************************/
+   }
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   if( *in == occ){
- {
+     *(alocc)='\0';
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+     s=++in;
-   double ***m;
+   }
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   if (s == t) {/* occ not found */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     *(alocc-(in-s))='\0';
-   m += NR_END;
+     in=s;
-   m -= nrl;
+   }
+   while ( *in != '\0'){
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     *blocc++ = *in++;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   }
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+   *blocc='\0';
+   return t;
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ {
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
-   m[nrl][ncl] += NR_END;
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   m[nrl][ncl] -= nll;
+      gives blocc="abcdef2ghi" and alocc="j".
-   for (j=ncl+1; j<=nch; j++)
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   */
+   char *s, *t;
-   for (i=nrl+1; i<=nrh; i++) {
+   t=in;s=in;
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   while (*in != '\0'){
-     for (j=ncl+1; j<=nch; j++)
+     while( *in == occ){
-       m[i][j]=m[i][j-1]+nlay;
+       *blocc++ = *in++;
-   }
+       s=in;
-   return m;
+     }
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+     *blocc++ = *in++;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   }
-   */
+   if (s == t) /* occ not found */
- }
+     *(blocc-(in-s))='\0';
+   else
- /*************************free ma3x ************************/
+     *(blocc-(in-s)-1)='\0';
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   in=s;
- {
+   while ( *in != '\0'){
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+     *alocc++ = *in++;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   }
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+   *alocc='\0';
+   return s;
- /*************** function subdirf ***********/
+ }
- char *subdirf(char fileres[])
- {
+ int nbocc(char *s, char occ)
-   /* Caution optionfilefiname is hidden */
+ {
-   strcpy(tmpout,optionfilefiname);
+   int i,j=0;
-   strcat(tmpout,"/"); /* Add to the right */
+   int lg=20;
-   strcat(tmpout,fileres);
+   i=0;
-   return tmpout;
+   lg=strlen(s);
- }
+   for(i=0; i<= lg; i++) {
+   if  (s[i] == occ ) j++;
- /*************** function subdirf2 ***********/
+   }
- char *subdirf2(char fileres[], char *preop)
+   return j;
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   strcpy(tmpout,optionfilefiname);
+ /* { */
-   strcat(tmpout,"/");
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   strcat(tmpout,preop);
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   strcat(tmpout,fileres);
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   return tmpout;
+ /*   int i,lg,j,p=0; */
- }
+ /*   i=0; */
+ /*   lg=strlen(t); */
- /*************** function subdirf3 ***********/
+ /*   for(j=0; j<=lg-1; j++) { */
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
- {
+ /*   } */
-   /* Caution optionfilefiname is hidden */
+ /*   for(j=0; j<p; j++) { */
-   strcpy(tmpout,optionfilefiname);
+ /*     (u[j] = t[j]); */
-   strcat(tmpout,"/");
+ /*   } */
-   strcat(tmpout,preop);
+ /*      u[p]='\0'; */
-   strcat(tmpout,preop2);
-   strcat(tmpout,fileres);
+ /*    for(j=0; j<= lg; j++) { */
-   return tmpout;
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
- }
+ /*   } */
+ /* } */
- /***************** f1dim *************************/
- extern int ncom;
+ #ifdef _WIN32
- extern double *pcom,*xicom;
+ char * strsep(char **pp, const char *delim)
- extern double (*nrfunc)(double []);
+ {
+   char *p, *q;
- double f1dim(double x)
- {
+   if ((p = *pp) == NULL)
-   int j;
+     return 0;
-   double f;
+   if ((q = strpbrk (p, delim)) != NULL)
-   double *xt;
+   {
+     *pp = q + 1;
-   xt=vector(1,ncom);
+     *q = '\0';
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   }
-   f=(*nrfunc)(xt);
+   else
-   free_vector(xt,1,ncom);
+     *pp = 0;
-   return f;
+   return p;
  }
+ #endif
- /*****************brent *************************/
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+ /********************** nrerror ********************/
- {
-   int iter;
+ void nrerror(char error_text[])
-   double a,b,d,etemp;
+ {
-   double fu,fv,fw,fx;
+   fprintf(stderr,"ERREUR ...\n");
-   double ftemp;
+   fprintf(stderr,"%s\n",error_text);
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   exit(EXIT_FAILURE);
-   double e=0.0;
+ }
+ /*********************** vector *******************/
-   a=(ax < cx ? ax : cx);
+ double *vector(int nl, int nh)
-   b=(ax > cx ? ax : cx);
+ {
-   x=w=v=bx;
+   double *v;
-   fw=fv=fx=(*f)(x);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   for (iter=1;iter<=ITMAX;iter++) {
+   if (!v) nrerror("allocation failure in vector");
-     xm=0.5*(a+b);
+   return v-nl+NR_END;
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ }
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     printf(".");fflush(stdout);
+ /************************ free vector ******************/
-     fprintf(ficlog,".");fflush(ficlog);
+ void free_vector(double*v, 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);
+   free((FREE_ARG)(v+nl-NR_END));
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ }
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- #endif
+ /************************ivector *******************************/
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ int *ivector(long nl,long nh)
-       *xmin=x;
+ {
-       return fx;
+   int *v;
-     }
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-     ftemp=fu;
+   if (!v) nrerror("allocation failure in ivector");
-     if (fabs(e) > tol1) {
+   return v-nl+NR_END;
-       r=(x-w)*(fx-fv);
+ }
-       q=(x-v)*(fx-fw);
-       p=(x-v)*q-(x-w)*r;
+ /******************free ivector **************************/
-       q=2.0*(q-r);
+ void free_ivector(int *v, long nl, long nh)
-       if (q > 0.0) p = -p;
+ {
-       q=fabs(q);
+   free((FREE_ARG)(v+nl-NR_END));
-       etemp=e;
+ }
-       e=d;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+ /************************lvector *******************************/
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ long *lvector(long nl,long nh)
-       else {
+ {
-         d=p/q;
+   long *v;
-         u=x+d;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-         if (u-a < tol2 || b-u < tol2)
+   if (!v) nrerror("allocation failure in ivector");
-           d=SIGN(tol1,xm-x);
+   return v-nl+NR_END;
-       }
+ }
-     } else {
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /******************free lvector **************************/
-     }
+ void free_lvector(long *v, long nl, long nh)
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ {
-     fu=(*f)(u);
+   free((FREE_ARG)(v+nl-NR_END));
-     if (fu <= fx) {
+ }
-       if (u >= x) a=x; else b=x;
-       SHFT(v,w,x,u)
+ /******************* imatrix *******************************/
-         SHFT(fv,fw,fx,fu)
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-         } else {
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-           if (u < x) a=u; else b=u;
+ {
-           if (fu <= fw || w == x) {
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-             v=w;
+   int **m;
-             w=u;
-             fv=fw;
+   /* allocate pointers to rows */
-             fw=fu;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-           } else if (fu <= fv || v == x || v == w) {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-             v=u;
+   m += NR_END;
-             fv=fu;
+   m -= nrl;
-           }
-         }
-   }
+   /* allocate rows and set pointers to them */
-   nrerror("Too many iterations in brent");
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   *xmin=x;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   return fx;
+   m[nrl] += NR_END;
- }
+   m[nrl] -= ncl;
- /****************** mnbrak ***********************/
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   /* return pointer to array of pointers to rows */
-             double (*func)(double))
+   return m;
- {
+ }
-   double ulim,u,r,q, dum;
-   double fu;
+ /****************** free_imatrix *************************/
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   *fa=(*func)(*ax);
+       int **m;
-   *fb=(*func)(*bx);
+       long nch,ncl,nrh,nrl;
-   if (*fb > *fa) {
+      /* free an int matrix allocated by imatrix() */
-     SHFT(dum,*ax,*bx,dum)
+ {
-       SHFT(dum,*fb,*fa,dum)
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-       }
+   free((FREE_ARG) (m+nrl-NR_END));
-   *cx=(*bx)+GOLD*(*bx-*ax);
+ }
-   *fc=(*func)(*cx);
-   while (*fb > *fc) {
+ /******************* matrix *******************************/
-     r=(*bx-*ax)*(*fb-*fc);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-     q=(*bx-*cx)*(*fb-*fa);
+ {
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   double **m;
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       fu=(*func)(u);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+   m += NR_END;
-       fu=(*func)(u);
+   m -= nrl;
-       if (fu < *fc) {
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-           SHFT(*fb,*fc,fu,(*func)(u))
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-           }
+   m[nrl] += NR_END;
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   m[nrl] -= ncl;
-       u=ulim;
-       fu=(*func)(u);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     } else {
+   return m;
-       u=(*cx)+GOLD*(*cx-*bx);
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-       fu=(*func)(u);
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-     }
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-     SHFT(*ax,*bx,*cx,u)
+    */
-       SHFT(*fa,*fb,*fc,fu)
+ }
-       }
- }
+ /*************************free matrix ************************/
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
- /*************** linmin ************************/
+ {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- int ncom;
+   free((FREE_ARG)(m+nrl-NR_END));
- double *pcom,*xicom;
+ }
- double (*nrfunc)(double []);
+ /******************* ma3x *******************************/
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
  {
-   double brent(double ax, double bx, double cx,
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-                double (*f)(double), double tol, double *xmin);
+   double ***m;
-   double f1dim(double x);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-               double *fc, double (*func)(double));
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   int j;
+   m += NR_END;
-   double xx,xmin,bx,ax;
+   m -= nrl;
-   double fx,fb,fa;
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   ncom=n;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   pcom=vector(1,n);
+   m[nrl] += NR_END;
-   xicom=vector(1,n);
+   m[nrl] -= ncl;
-   nrfunc=func;
-   for (j=1;j<=n;j++) {
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     pcom[j]=p[j];
-     xicom[j]=xi[j];
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   }
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   ax=0.0;
+   m[nrl][ncl] += NR_END;
-   xx=1.0;
+   m[nrl][ncl] -= nll;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   for (j=ncl+1; j<=nch; j++)
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+     m[nrl][j]=m[nrl][j-1]+nlay;
- #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   for (i=nrl+1; i<=nrh; i++) {
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- #endif
+     for (j=ncl+1; j<=nch; j++)
-   for (j=1;j<=n;j++) {
+       m[i][j]=m[i][j-1]+nlay;
-     xi[j] *= xmin;
+   }
-     p[j] += xi[j];
+   return m;
-   }
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   free_vector(xicom,1,n);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   free_vector(pcom,1,n);
+   */
  }
- char *asc_diff_time(long time_sec, char ascdiff[])
+ /*************************free ma3x ************************/
- {
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   long sec_left, days, hours, minutes;
+ {
-   days = (time_sec) / (60*60*24);
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   sec_left = (time_sec) % (60*60*24);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   hours = (sec_left) / (60*60) ;
+   free((FREE_ARG)(m+nrl-NR_END));
-   sec_left = (sec_left) %(60*60);
+ }
-   minutes = (sec_left) /60;
-   sec_left = (sec_left) % (60);
+ /*************** function subdirf ***********/
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ char *subdirf(char fileres[])
-   return ascdiff;
+ {
- }
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
- /*************** powell ************************/
+   strcat(tmpout,"/"); /* Add to the right */
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   strcat(tmpout,fileres);
-             double (*func)(double []))
+   return tmpout;
- {
+ }
-   void linmin(double p[], double xi[], int n, double *fret,
-               double (*func)(double []));
+ /*************** function subdirf2 ***********/
-   int i,ibig,j;
+ char *subdirf2(char fileres[], char *preop)
-   double del,t,*pt,*ptt,*xit;
+ {
-   double fp,fptt;
-   double *xits;
+   /* Caution optionfilefiname is hidden */
-   int niterf, itmp;
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
-   pt=vector(1,n);
+   strcat(tmpout,preop);
-   ptt=vector(1,n);
+   strcat(tmpout,fileres);
-   xit=vector(1,n);
+   return tmpout;
-   xits=vector(1,n);
+ }
-   *fret=(*func)(p);
-   for (j=1;j<=n;j++) pt[j]=p[j];
+ /*************** function subdirf3 ***********/
-   for (*iter=1;;++(*iter)) {
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-     fp=(*fret);
+ {
-     ibig=0;
-     del=0.0;
+   /* Caution optionfilefiname is hidden */
-     last_time=curr_time;
+   strcpy(tmpout,optionfilefiname);
-     (void) gettimeofday(&curr_time,&tzp);
+   strcat(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);
+   strcat(tmpout,preop);
-     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);
+   strcat(tmpout,preop2);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+   strcat(tmpout,fileres);
-    for (i=1;i<=n;i++) {
+   return tmpout;
-       printf(" %d %.12f",i, p[i]);
+ }
-       fprintf(ficlog," %d %.12lf",i, p[i]);
-       fprintf(ficrespow," %.12lf", p[i]);
+ char *asc_diff_time(long time_sec, char ascdiff[])
-     }
+ {
-     printf("\n");
+   long sec_left, days, hours, minutes;
-     fprintf(ficlog,"\n");
+   days = (time_sec) / (60*60*24);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   sec_left = (time_sec) % (60*60*24);
-     if(*iter <=3){
+   hours = (sec_left) / (60*60) ;
-       tm = *localtime(&curr_time.tv_sec);
+   sec_left = (sec_left) %(60*60);
-       strcpy(strcurr,asctime(&tm));
+   minutes = (sec_left) /60;
- /*       asctime_r(&tm,strcurr); */
+   sec_left = (sec_left) % (60);
-       forecast_time=curr_time;
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-       itmp = strlen(strcurr);
+   return ascdiff;
-       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);
+ /***************** f1dim *************************/
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+ extern int ncom;
-       for(niterf=10;niterf<=30;niterf+=10){
+ extern double *pcom,*xicom;
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ extern double (*nrfunc)(double []);
-         tmf = *localtime(&forecast_time.tv_sec);
- /*      asctime_r(&tmf,strfor); */
+ double f1dim(double x)
-         strcpy(strfor,asctime(&tmf));
+ {
-         itmp = strlen(strfor);
+   int j;
-         if(strfor[itmp-1]=='\n')
+   double f;
-         strfor[itmp-1]='\0';
+   double *xt;
-         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);
-         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);
+   xt=vector(1,ncom);
-       }
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-     }
+   f=(*nrfunc)(xt);
-     for (i=1;i<=n;i++) {
+   free_vector(xt,1,ncom);
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   return f;
-       fptt=(*fret);
+ }
- #ifdef DEBUG
-       printf("fret=%lf \n",*fret);
+ /*****************brent *************************/
-       fprintf(ficlog,"fret=%lf \n",*fret);
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- #endif
+ {
-       printf("%d",i);fflush(stdout);
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-       linmin(p,xit,n,fret,func);
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
-       if (fabs(fptt-(*fret)) > del) {
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
-         del=fabs(fptt-(*fret));
+    * returned function value.
-         ibig=i;
+   */
-       }
+   int iter;
- #ifdef DEBUG
+   double a,b,d,etemp;
-       printf("%d %.12e",i,(*fret));
+   double fu=0,fv,fw,fx;
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   double ftemp=0.;
-       for (j=1;j<=n;j++) {
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   double e=0.0;
-         printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   a=(ax < cx ? ax : cx);
-       }
+   b=(ax > cx ? ax : cx);
-       for(j=1;j<=n;j++) {
+   x=w=v=bx;
-         printf(" p=%.12e",p[j]);
+   fw=fv=fx=(*f)(x);
-         fprintf(ficlog," p=%.12e",p[j]);
+   for (iter=1;iter<=ITMAX;iter++) {
-       }
+     xm=0.5*(a+b);
-       printf("\n");
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-       fprintf(ficlog,"\n");
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
- #endif
+     printf(".");fflush(stdout);
-     }
+     fprintf(ficlog,".");fflush(ficlog);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+ #ifdef DEBUGBRENT
- #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);
-       int k[2],l;
+     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);
-       k[0]=1;
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-       k[1]=-1;
+ #endif
-       printf("Max: %.12e",(*func)(p));
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       *xmin=x;
-       for (j=1;j<=n;j++) {
+       return fx;
-         printf(" %.12e",p[j]);
+     }
-         fprintf(ficlog," %.12e",p[j]);
+     ftemp=fu;
-       }
+     if (fabs(e) > tol1) {
-       printf("\n");
+       r=(x-w)*(fx-fv);
-       fprintf(ficlog,"\n");
+       q=(x-v)*(fx-fw);
-       for(l=0;l<=1;l++) {
+       p=(x-v)*q-(x-w)*r;
-         for (j=1;j<=n;j++) {
+       q=2.0*(q-r);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       if (q > 0.0) p = -p;
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       q=fabs(q);
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       etemp=e;
-         }
+       e=d;
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       }
+       else {
- #endif
+         d=p/q;
+         u=x+d;
+         if (u-a < tol2 || b-u < tol2)
-       free_vector(xit,1,n);
+           d=SIGN(tol1,xm-x);
-       free_vector(xits,1,n);
+       }
-       free_vector(ptt,1,n);
+     } else {
-       free_vector(pt,1,n);
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       return;
+     }
-     }
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     fu=(*f)(u);
-     for (j=1;j<=n;j++) {
+     if (fu <= fx) {
-       ptt[j]=2.0*p[j]-pt[j];
+       if (u >= x) a=x; else b=x;
-       xit[j]=p[j]-pt[j];
+       SHFT(v,w,x,u)
-       pt[j]=p[j];
+       SHFT(fv,fw,fx,fu)
-     }
+     } else {
-     fptt=(*func)(ptt);
+       if (u < x) a=u; else b=u;
-     if (fptt < fp) {
+       if (fu <= fw || w == x) {
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+         v=w;
-       if (t < 0.0) {
+         w=u;
-         linmin(p,xit,n,fret,func);
+         fv=fw;
-         for (j=1;j<=n;j++) {
+         fw=fu;
-           xi[j][ibig]=xi[j][n];
+       } else if (fu <= fv || v == x || v == w) {
-           xi[j][n]=xit[j];
+         v=u;
-         }
+         fv=fu;
- #ifdef DEBUG
+       }
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     }
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   }
-         for(j=1;j<=n;j++){
+   nrerror("Too many iterations in brent");
-           printf(" %.12e",xit[j]);
+   *xmin=x;
-           fprintf(ficlog," %.12e",xit[j]);
+   return fx;
-         }
+ }
-         printf("\n");
-         fprintf(ficlog,"\n");
+ /****************** mnbrak ***********************/
- #endif
-       }
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-     }
+             double (*func)(double))
-   }
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
- }
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
- /**** Prevalence limit (stable or period prevalence)  ****************/
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
+    */
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   double ulim,u,r,q, dum;
- {
+   double fu;
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-      matrix by transitions matrix until convergence is reached */
+   double scale=10.;
+   int iterscale=0;
-   int i, ii,j,k;
-   double min, max, maxmin, maxmax,sumnew=0.;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
-   double **matprod2();
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
-   double **out, cov[NCOVMAX], **pmij();
-   double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-     for (j=1;j<=nlstate+ndeath;j++){
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* } */
-     }
+   if (*fb > *fa) {
-    cov[1]=1.;
+     SHFT(dum,*ax,*bx,dum)
+     SHFT(dum,*fb,*fa,dum)
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   }
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+   *cx=(*bx)+GOLD*(*bx-*ax);
-     newm=savm;
+   *fc=(*func)(*cx);
-     /* Covariates have to be included here again */
+ #ifdef DEBUG
-      cov[2]=agefin;
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-       for (k=1; k<=cptcovn;k++) {
+ #endif
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
-         /*      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]]);*/
+     r=(*bx-*ax)*(*fb-*fc);
-       }
+     q=(*bx-*cx)*(*fb-*fa);
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       for (k=1; k<=cptcovprod;k++)
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+       fu=(*func)(u);
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+ #ifdef DEBUG
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+       /* f(x)=A(x-u)**2+f(u) */
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+       double A, fparabu;
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-     savm=oldm;
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-     oldm=newm;
+       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);
-     maxmax=0.;
+       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);
-     for(j=1;j<=nlstate;j++){
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-       min=1.;
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-       max=0.;
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-       for(i=1; i<=nlstate; i++) {
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-         sumnew=0;
+ #endif
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+ #ifdef MNBRAKORIGINAL
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+ #else
-         max=FMAX(max,prlim[i][j]);
+ /*       if (fu > *fc) { */
-         min=FMIN(min,prlim[i][j]);
+ /* #ifdef DEBUG */
-       }
+ /*       printf("mnbrak4  fu > fc \n"); */
-       maxmin=max-min;
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
-       maxmax=FMAX(maxmax,maxmin);
+ /* #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 *\\/  *\/ */
-     if(maxmax < ftolpl){
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
-       return prlim;
+ /*      dum=u; /\* Shifting c and u *\/ */
-     }
+ /*      u = *cx; */
-   }
+ /*      *cx = dum; */
- }
+ /*      dum = fu; */
+ /*      fu = *fc; */
- /*************** transition probabilities ***************/
+ /*      *fc =dum; */
+ /*       } else { /\* end *\/ */
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ /* #ifdef DEBUG */
- {
+ /*       printf("mnbrak3  fu < fc \n"); */
-   double s1, s2;
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-   /*double t34;*/
+ /* #endif */
-   int i,j,j1, nc, ii, jj;
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
-     for(i=1; i<= nlstate; i++){
+ /*      *cx = dum; */
-       for(j=1; j<i;j++){
+ /*      dum = fu; */
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ /*      fu = *fc; */
-           /*s2 += param[i][j][nc]*cov[nc];*/
+ /*      *fc =dum; */
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*       } */
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ #ifdef DEBUG
-         }
+       printf("mnbrak34  fu < or >= fc \n");
-         ps[i][j]=s2;
+       fprintf(ficlog, "mnbrak34 fu < fc\n");
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ #endif
-       }
+       dum=u; /* Shifting c and u */
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       u = *cx;
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       *cx = dum;
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       dum = fu;
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+       fu = *fc;
-         }
+       *fc =dum;
-         ps[i][j]=s2;
+ #endif
-       }
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-     }
+ #ifdef DEBUG
-     /*ps[3][2]=1;*/
+       printf("mnbrak2  u after c but before ulim\n");
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
-     for(i=1; i<= nlstate; i++){
+ #endif
-       s1=0;
+       fu=(*func)(u);
-       for(j=1; j<i; j++)
+       if (fu < *fc) {
-         s1+=exp(ps[i][j]);
+ #ifdef DEBUG
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
-         s1+=exp(ps[i][j]);
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
-       ps[i][i]=1./(s1+1.);
+ #endif
-       for(j=1; j<i; j++)
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         SHFT(*fb,*fc,fu,(*func)(u))
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       }
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+ #ifdef DEBUG
-     } /* end i */
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ #endif
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       u=ulim;
-         ps[ii][jj]=0;
+       fu=(*func)(u);
-         ps[ii][ii]=1;
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
-       }
+ #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
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       u=(*cx)+GOLD*(*cx-*bx);
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       fu=(*func)(u);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+     } /* end tests */
- /*       } */
+     SHFT(*ax,*bx,*cx,u)
- /*       printf("\n "); */
+     SHFT(*fa,*fb,*fc,fu)
- /*        } */
+ #ifdef DEBUG
- /*        printf("\n ");printf("%lf ",cov[2]); */
+       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);
-        /*
+       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);
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ #endif
-       goto end;*/
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-     return ps;
+ }
- }
+ /*************** linmin ************************/
- /**************** Product of 2 matrices ******************/
+ /* 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 ,
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
- {
+ the value of func at the returned location p . This is actually all accomplished by calling the
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ routines mnbrak and brent .*/
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+ int ncom;
-   /* in, b, out are matrice of pointers which should have been initialized
+ double *pcom,*xicom;
-      before: only the contents of out is modified. The function returns
+ double (*nrfunc)(double []);
-      a pointer to pointers identical to out */
-   long i, j, k;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-   for(i=nrl; i<= nrh; i++)
+ {
-     for(k=ncolol; k<=ncoloh; k++)
+   double brent(double ax, double bx, double cx,
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+                double (*f)(double), double tol, double *xmin);
-         out[i][k] +=in[i][j]*b[j][k];
+   double f1dim(double x);
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-   return out;
+               double *fc, double (*func)(double));
- }
+   int j;
+   double xx,xmin,bx,ax;
+   double fx,fb,fa;
- /************* Higher Matrix Product ***************/
+   double scale=10., axs, xxs, xxss; /* Scale added for infinity */
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
- {
+   ncom=n;
-   /* Computes the transition matrix starting at age 'age' over
+   pcom=vector(1,n);
-      'nhstepm*hstepm*stepm' months (i.e. until
+   xicom=vector(1,n);
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+   nrfunc=func;
-      nhstepm*hstepm matrices.
+   for (j=1;j<=n;j++) {
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     pcom[j]=p[j];
-      (typically every 2 years instead of every month which is too big
+     xicom[j]=xi[j];
-      for the memory).
+   }
-      Model is determined by parameters x and covariates have to be
-      included manually here.
+   /* axs=0.0; */
+   /* xxss=1; /\* 1 and using scale *\/ */
-      */
+   xxs=1;
+   /* do{ */
-   int i, j, d, h, k;
+     ax=0.;
-   double **out, cov[NCOVMAX];
+     xx= xxs;
-   double **newm;
+     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) */
-   /* Hstepm could be zero and should return the unit matrix */
+     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
-   for (i=1;i<=nlstate+ndeath;i++)
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
-     for (j=1;j<=nlstate+ndeath;j++){
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
-     }
+   /*   if (fx != fx){ */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
-   for(h=1; h <=nhstepm; h++){
+   /*    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(d=1; d <=hstepm; d++){
+   /*   } */
-       newm=savm;
+   /* }while(fx != fx); */
-       /* Covariates have to be included here again */
-       cov[1]=1.;
+ #ifdef DEBUGLINMIN
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+   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);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ #endif
-       for (k=1; k<=cptcovage;k++)
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
-       for (k=1; k<=cptcovprod;k++)
+   /* fmin = f(p[j] + xmin * xi[j]) */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
+ #ifdef DEBUG
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+ #endif
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef DEBUGLINMIN
-       savm=oldm;
+   printf("linmin end ");
-       oldm=newm;
+ #endif
-     }
+   for (j=1;j<=n;j++) {
-     for(i=1; i<=nlstate+ndeath; i++)
+     /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
-       for(j=1;j<=nlstate+ndeath;j++) {
+     xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
-         po[i][j][h]=newm[i][j];
+     /* if(xxs <1.0) */
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+     /*   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 ); */
-          */
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-       }
+   }
-   } /* end h */
+   /* printf("\n"); */
-   return po;
+ #ifdef DEBUGLINMIN
- }
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   for (j=1;j<=n;j++) {
+     printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
- /*************** log-likelihood *************/
+     if(j % ncovmodel == 0)
- double func( double *x)
+       printf("\n");
- {
+   }
-   int i, ii, j, k, mi, d, kk;
+ #endif
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   free_vector(xicom,1,n);
-   double **out;
+   free_vector(pcom,1,n);
-   double sw; /* Sum of weights */
+ }
-   double lli; /* Individual log likelihood */
-   int s1, s2;
-   double bbh, survp;
+ /*************** powell ************************/
-   long ipmx;
+ /*
-   /*extern weight */
+ Minimization of a function func of n variables. Input consists of an initial starting point
-   /* We are differentiating ll according to initial status */
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-   /*for(i=1;i<imx;i++)
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-     printf(" %d\n",s[4][i]);
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-   */
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-   cov[1]=1.;
+  */
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+             double (*func)(double []))
+ {
-   if(mle==1){
+   void linmin(double p[], double xi[], int n, double *fret,
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+               double (*func)(double []));
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   int i,ibig,j;
-       for(mi=1; mi<= wav[i]-1; mi++){
+   double del,t,*pt,*ptt,*xit;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   double directest;
-           for (j=1;j<=nlstate+ndeath;j++){
+   double fp,fptt;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   double *xits;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   int niterf, itmp;
-           }
-         for(d=0; d<dh[mi][i]; d++){
+   pt=vector(1,n);
-           newm=savm;
+   ptt=vector(1,n);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   xit=vector(1,n);
-           for (kk=1; kk<=cptcovage;kk++) {
+   xits=vector(1,n);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   *fret=(*func)(p);
-           }
+   for (j=1;j<=n;j++) pt[j]=p[j];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     rcurr_time = time(NULL);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   for (*iter=1;;++(*iter)) {
-           savm=oldm;
+     fp=(*fret); /* From former iteration or initial value */
-           oldm=newm;
+     ibig=0;
-         } /* end mult */
+     del=0.0;
+     rlast_time=rcurr_time;
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     /* (void) gettimeofday(&curr_time,&tzp); */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     rcurr_time = time(NULL);
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     curr_time = *localtime(&rcurr_time);
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+     for (i=1;i<=n;i++) {
-          * probability in order to take into account the bias as a fraction of the way
+       printf(" %d %.12f",i, p[i]);
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-          * -stepm/2 to stepm/2 .
+       fprintf(ficrespow," %.12lf", p[i]);
-          * For stepm=1 the results are the same as for previous versions of Imach.
+     }
-          * For stepm > 1 the results are less biased than in previous versions.
+     printf("\n");
-          */
+     fprintf(ficlog,"\n");
-         s1=s[mw[mi][i]][i];
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-         s2=s[mw[mi+1][i]][i];
+     if(*iter <=3){
-         bbh=(double)bh[mi][i]/(double)stepm;
+       tml = *localtime(&rcurr_time);
-         /* bias bh is positive if real duration
+       strcpy(strcurr,asctime(&tml));
-          * is higher than the multiple of stepm and negative otherwise.
+       rforecast_time=rcurr_time;
-          */
+       itmp = strlen(strcurr);
-         /* 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(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-         if( s2 > nlstate){
+         strcurr[itmp-1]='\0';
-           /* i.e. if s2 is a death state and if the date of death is known
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-              then the contribution to the likelihood is the probability to
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-              die between last step unit time and current  step unit time,
+       for(niterf=10;niterf<=30;niterf+=10){
-              which is also equal to probability to die before dh
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-              minus probability to die before dh-stepm .
+         forecast_time = *localtime(&rforecast_time);
-              In version up to 0.92 likelihood was computed
+         strcpy(strfor,asctime(&forecast_time));
-         as if date of death was unknown. Death was treated as any other
+         itmp = strlen(strfor);
-         health state: the date of the interview describes the actual state
+         if(strfor[itmp-1]=='\n')
-         and not the date of a change in health state. The former idea was
+         strfor[itmp-1]='\0';
-         to consider that at each interview the state was recorded
+         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);
-         (healthy, disable or death) and IMaCh was corrected; but when we
+         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);
-         introduced the exact date of death then we should have modified
+       }
-         the contribution of an exact death to the likelihood. This new
+     }
-         contribution is smaller and very dependent of the step unit
+     for (i=1;i<=n;i++) { /* For each direction i */
-         stepm. It is no more the probability to die between last interview
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-         and month of death but the probability to survive from last
+       fptt=(*fret);
-         interview up to one month before death multiplied by the
+ #ifdef DEBUG
-         probability to die within a month. Thanks to Chris
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         Jackson for correcting this bug.  Former versions increased
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         mortality artificially. The bad side is that we add another loop
+ #endif
-         which slows down the processing. The difference can be up to 10%
+           printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-         lower mortality.
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-           */
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-           lli=log(out[s1][s2] - savm[s1][s2]);
+                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
+         /* because that direction will be replaced unless the gain del is small */
-         } else if  (s2==-2) {
+         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-           for (j=1,survp=0. ; j<=nlstate; j++)
+         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         /* with the new direction. */
-           /*survp += out[s1][j]; */
+         del=fabs(fptt-(*fret));
-           lli= log(survp);
+         ibig=i;
-         }
+       }
+ #ifdef DEBUG
-         else if  (s2==-4) {
+       printf("%d %.12e",i,(*fret));
-           for (j=3,survp=0. ; j<=nlstate; j++)
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for (j=1;j<=n;j++) {
-           lli= log(survp);
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         }
+         printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-         else if  (s2==-5) {
+       }
-           for (j=1,survp=0. ; j<=2; j++)
+       for(j=1;j<=n;j++) {
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         printf(" p(%d)=%.12e",j,p[j]);
-           lli= log(survp);
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-         }
+       }
+       printf("\n");
-         else{
+       fprintf(ficlog,"\n");
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ #endif
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+     } /* end loop on each direction i */
-         }
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-         /*if(lli ==000.0)*/
+     /* New value of last point Pn is not computed, P(n-1) */
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-         ipmx +=1;
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
-         sw += weight[i];
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
-       } /* end of wave */
+       /* decreased of more than 3.84  */
-     } /* end of individual */
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
-   }  else if(mle==2){
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* By adding 10 parameters more the gain should be 18.31 */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+       /* Starting the program with initial values given by a former maximization will simply change */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-           for (j=1;j<=nlstate+ndeath;j++){
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
-             oldm[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.  */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef DEBUG
-           }
+       int k[2],l;
-         for(d=0; d<=dh[mi][i]; d++){
+       k[0]=1;
-           newm=savm;
+       k[1]=-1;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       printf("Max: %.12e",(*func)(p));
-           for (kk=1; kk<=cptcovage;kk++) {
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       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]);
-         bbh=(double)bh[mi][i]/(double)stepm;
+           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= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         }
-         ipmx +=1;
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         sw += weight[i];
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       }
-       } /* end of wave */
+ #endif
-     } /* end of individual */
-   }  else if(mle==3){  /* exponential inter-extrapolation */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       free_vector(xit,1,n);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       free_vector(xits,1,n);
-       for(mi=1; mi<= wav[i]-1; mi++){
+       free_vector(ptt,1,n);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       free_vector(pt,1,n);
-           for (j=1;j<=nlstate+ndeath;j++){
+       return;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     } /* enough precision */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-           }
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-         for(d=0; d<dh[mi][i]; d++){
+       ptt[j]=2.0*p[j]-pt[j];
-           newm=savm;
+       xit[j]=p[j]-pt[j];
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       pt[j]=p[j];
-           for (kk=1; kk<=cptcovage;kk++) {
+     }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     fptt=(*func)(ptt); /* f_3 */
-           }
+ #ifdef POWELLF1F3
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ #else
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-           savm=oldm;
+ #endif
-           oldm=newm;
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-         } /* end mult */
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-         s1=s[mw[mi][i]][i];
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-         s2=s[mw[mi+1][i]][i];
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-         bbh=(double)bh[mi][i]/(double)stepm;
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-         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 */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-         ipmx +=1;
+ #ifdef NRCORIGINAL
-         sw += weight[i];
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ #else
-       } /* end of wave */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
-     } /* end of individual */
+       t= t- del*SQR(fp-fptt);
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+ #endif
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #ifdef DEBUG
-       for(mi=1; mi<= wav[i]-1; mi++){
+       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);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       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);
-           for (j=1;j<=nlstate+ndeath;j++){
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-           }
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-         for(d=0; d<dh[mi][i]; d++){
+       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);
-           newm=savm;
+       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);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #endif
-           for (kk=1; kk<=cptcovage;kk++) {
+ #ifdef POWELLORIGINAL
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       if (t < 0.0) { /* Then we use it for new direction */
-           }
+ #else
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-           savm=oldm;
+         fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
-           oldm=newm;
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-         } /* end mult */
+       }
+       if (directest < 0.0) { /* Then we use it for new direction */
-         s1=s[mw[mi][i]][i];
+ #endif
-         s2=s[mw[mi+1][i]][i];
+ #ifdef DEBUGLINMIN
-         if( s2 > nlstate){
+         printf("Before linmin in direction P%d-P0\n",n);
-           lli=log(out[s1][s2] - savm[s1][s2]);
+         for (j=1;j<=n;j++) {
-         }else{
+           printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+           if(j % ncovmodel == 0)
-         }
+             printf("\n");
-         ipmx +=1;
+         }
-         sw += weight[i];
+ #endif
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+ #ifdef DEBUGLINMIN
-       } /* end of wave */
+         for (j=1;j<=n;j++) {
-     } /* end of individual */
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+           if(j % ncovmodel == 0)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+             printf("\n");
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         }
-       for(mi=1; mi<= wav[i]-1; mi++){
+ #endif
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=n;j++) {
-           for (j=1;j<=nlstate+ndeath;j++){
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
-           }
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-         for(d=0; d<dh[mi][i]; d++){
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #ifdef DEBUG
-           for (kk=1; kk<=cptcovage;kk++) {
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-           }
+         for(j=1;j<=n;j++){
+           printf(" %.12e",xit[j]);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           fprintf(ficlog," %.12e",xit[j]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         }
-           savm=oldm;
+         printf("\n");
-           oldm=newm;
+         fprintf(ficlog,"\n");
-         } /* end mult */
+ #endif
+       } /* end of t or directest negative */
-         s1=s[mw[mi][i]][i];
+ #ifdef POWELLF1F3
-         s2=s[mw[mi+1][i]][i];
+ #else
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+     } /* end if (fptt < fp)  */
-         ipmx +=1;
+ #endif
-         sw += weight[i];
+   } /* loop iteration */
-         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]);*/
-       } /* end of wave */
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-     } /* end of individual */
-   } /* End of if */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ {
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+      matrix by transitions matrix until convergence is reached */
-   return -l;
- }
+   int i, ii,j,k;
+   double min, max, maxmin, maxmax,sumnew=0.;
- /*************** log-likelihood *************/
+   /* double **matprod2(); */ /* test */
- double funcone( double *x)
+   double **out, cov[NCOVMAX+1], **pmij();
- {
+   double **newm;
-   /* Same as likeli but slower because of a lot of printf and if */
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-   double **out;
+     for (j=1;j<=nlstate+ndeath;j++){
-   double lli; /* Individual log likelihood */
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double llt;
+     }
-   int s1, s2;
-   double bbh, survp;
+   cov[1]=1.;
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-   /*for(i=1;i<imx;i++)
+     newm=savm;
-     printf(" %d\n",s[4][i]);
+     /* Covariates have to be included here again */
-   */
+     cov[2]=agefin;
-   cov[1]=1.;
+     if(nagesqr==1)
+       cov[3]= agefin*agefin;;
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+     for (k=1; k<=cptcovn;k++) {
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     }
-     for(mi=1; mi<= wav[i]-1; mi++){
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
-         for (j=1;j<=nlstate+ndeath;j++){
+     for (k=1; k<=cptcovprod;k++) /* Useless */
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       for(d=0; d<dh[mi][i]; d++){
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-         newm=savm;
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         for (kk=1; kk<=cptcovage;kk++) {
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-         }
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     savm=oldm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     oldm=newm;
-         savm=oldm;
+     maxmax=0.;
-         oldm=newm;
+     for(j=1;j<=nlstate;j++){
-       } /* end mult */
+       min=1.;
+       max=0.;
-       s1=s[mw[mi][i]][i];
+       for(i=1; i<=nlstate; i++) {
-       s2=s[mw[mi+1][i]][i];
+         sumnew=0;
-       bbh=(double)bh[mi][i]/(double)stepm;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-       /* bias is positive if real duration
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-        * is higher than the multiple of stepm and negative otherwise.
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-        */
+         max=FMAX(max,prlim[i][j]);
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         min=FMIN(min,prlim[i][j]);
-         lli=log(out[s1][s2] - savm[s1][s2]);
+       }
-       } else if  (s2==-2) {
+       maxmin=max-min;
-         for (j=1,survp=0. ; j<=nlstate; j++)
+       maxmax=FMAX(maxmax,maxmin);
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     } /* j loop */
-         lli= log(survp);
+     if(maxmax < ftolpl){
-       }else if (mle==1){
+       return prlim;
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+     }
-       } else if(mle==2){
+   } /* age loop */
-         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 */
+   return prlim; /* should not reach here */
-       } 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 */
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+ /*************** transition probabilities ***************/
-         lli=log(out[s1][s2]); /* Original formula */
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-         lli=log(out[s1][s2]); /* Original formula */
+ {
-       } /* End of if */
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-       ipmx +=1;
+      computes the probability to be observed in state j being in state i by appying the
-       sw += weight[i];
+      model to the ncovmodel covariates (including constant and age).
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
- /*       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]); */
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-       if(globpr){
+      ncth covariate in the global vector x is given by the formula:
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-  %11.6f %11.6f %11.6f ", \
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-           llt +=ll[k]*gipmx/gsw;
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+   */
-         }
+   double s1, lnpijopii;
-         fprintf(ficresilk," %10.6f\n", -llt);
+   /*double t34;*/
-       }
+   int i,j, nc, ii, jj;
-     } /* end of wave */
-   } /* end of individual */
+     for(i=1; i<= nlstate; i++){
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+       for(j=1; j<i;j++){
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-   if(globpr==0){ /* First time we count the contributions and weights */
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-     gipmx=ipmx;
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     gsw=sw;
+         }
-   }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   return -l;
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
- }
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- /*************** function likelione ***********/
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
- {
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-   /* This routine should help understanding what is done with
+         }
-      the selection of individuals/waves and
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-      to check the exact contribution to the likelihood.
+       }
-      Plotting could be done.
+     }
-    */
-   int k;
+     for(i=1; i<= nlstate; i++){
+       s1=0;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+       for(j=1; j<i; j++){
-     strcpy(fileresilk,"ilk");
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-     strcat(fileresilk,fileres);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       }
-       printf("Problem with resultfile: %s\n", fileresilk);
+       for(j=i+1; j<=nlstate+ndeath; j++){
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+         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); */
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+       }
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+       ps[i][i]=1./(s1+1.);
-     for(k=1; k<=nlstate; k++)
+       /* Computing other pijs */
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+       for(j=1; j<i; j++)
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-   }
+       for(j=i+1; j<=nlstate+ndeath; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-   *fretone=(*funcone)(p);
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   if(*globpri !=0){
+     } /* end i */
-     fclose(ficresilk);
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     fflush(fichtm);
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-   }
+         ps[ii][jj]=0;
-   return;
+         ps[ii][ii]=1;
- }
+       }
+     }
- /*********** Maximum Likelihood Estimation ***************/
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
- {
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-   int i,j, iter;
+     /*   } */
-   double **xi;
+     /*   printf("\n "); */
-   double fret;
+     /* } */
-   double fretone; /* Only one call to likelihood */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-   /*  char filerespow[FILENAMELENGTH];*/
+     /*
-   xi=matrix(1,npar,1,npar);
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   for (i=1;i<=npar;i++)
+       goto end;*/
-     for (j=1;j<=npar;j++)
+     return ps;
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+ }
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   strcpy(filerespow,"pow");
+ /**************** Product of 2 matrices ******************/
-   strcat(filerespow,fileres);
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-     printf("Problem with resultfile: %s\n", filerespow);
+ {
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-   }
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   /* in, b, out are matrice of pointers which should have been initialized
-   for (i=1;i<=nlstate;i++)
+      before: only the contents of out is modified. The function returns
-     for(j=1;j<=nlstate+ndeath;j++)
+      a pointer to pointers identical to out */
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   int i, j, k;
-   fprintf(ficrespow,"\n");
+   for(i=nrl; i<= nrh; i++)
+     for(k=ncolol; k<=ncoloh; k++){
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+       out[i][k]=0.;
+       for(j=ncl; j<=nch; j++)
-   free_matrix(xi,1,npar,1,npar);
+         out[i][k] +=in[i][j]*b[j][k];
-   fclose(ficrespow);
+     }
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   return out;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+ }
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
- }
+ /************* Higher Matrix Product ***************/
- /**** Computes Hessian and covariance matrix ***/
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ {
- {
+   /* Computes the transition matrix starting at age 'age' over
-   double  **a,**y,*x,pd;
+      'nhstepm*hstepm*stepm' months (i.e. until
-   double **hess;
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   int i, j,jk;
+      nhstepm*hstepm matrices.
-   int *indx;
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+      (typically every 2 years instead of every month which is too big
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+      for the memory).
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+      Model is determined by parameters x and covariates have to be
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+      included manually here.
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   double gompertz(double p[]);
+      */
-   hess=matrix(1,npar,1,npar);
+   int i, j, d, h, k;
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+   double **out, cov[NCOVMAX+1];
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+   double **newm;
-   for (i=1;i<=npar;i++){
+   double agexact;
-     printf("%d",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-     /*  printf(" %f ",p[i]);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+     }
-   }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
-   for (i=1;i<=npar;i++) {
+     for(d=1; d <=hstepm; d++){
-     for (j=1;j<=npar;j++)  {
+       newm=savm;
-       if (j>i) {
+       /* Covariates have to be included here again */
-         printf(".%d%d",i,j);fflush(stdout);
+       cov[1]=1.;
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       cov[2]=agexact;
+       if(nagesqr==1)
-         hess[j][i]=hess[i][j];
+         cov[3]= agexact*agexact;
-         /*printf(" %lf ",hess[i][j]);*/
+       for (k=1; k<=cptcovn;k++)
-       }
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-     }
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-   }
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   printf("\n");
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
-   fprintf(ficlog,"\n");
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-   a=matrix(1,npar,1,npar);
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-   y=matrix(1,npar,1,npar);
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-   x=vector(1,npar);
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-   indx=ivector(1,npar);
+       savm=oldm;
-   for (i=1;i<=npar;i++)
+       oldm=newm;
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+     }
-   ludcmp(a,npar,indx,&pd);
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
-   for (j=1;j<=npar;j++) {
+         po[i][j][h]=newm[i][j];
-     for (i=1;i<=npar;i++) x[i]=0;
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-     x[j]=1;
+       }
-     lubksb(a,npar,indx,x);
+     /*printf("h=%d ",h);*/
-     for (i=1;i<=npar;i++){
+   } /* end h */
-       matcov[i][j]=x[i];
+ /*     printf("\n H=%d \n",h); */
-     }
+   return po;
-   }
+ }
-   printf("\n#Hessian matrix#\n");
+ #ifdef NLOPT
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-   for (i=1;i<=npar;i++) {
+   double fret;
-     for (j=1;j<=npar;j++) {
+   double *xt;
-       printf("%.3e ",hess[i][j]);
+   int j;
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   myfunc_data *d2 = (myfunc_data *) pd;
-     }
+ /* xt = (p1-1); */
-     printf("\n");
+   xt=vector(1,n);
-     fprintf(ficlog,"\n");
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   }
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-   /* Recompute Inverse */
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-   for (i=1;i<=npar;i++)
+   printf("Function = %.12lf ",fret);
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   ludcmp(a,npar,indx,&pd);
+   printf("\n");
+  free_vector(xt,1,n);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   return fret;
+ }
-   for (j=1;j<=npar;j++) {
+ #endif
-     for (i=1;i<=npar;i++) x[i]=0;
-     x[j]=1;
+ /*************** log-likelihood *************/
-     lubksb(a,npar,indx,x);
+ double func( double *x)
-     for (i=1;i<=npar;i++){
+ {
-       y[i][j]=x[i];
+   int i, ii, j, k, mi, d, kk;
-       printf("%.3e ",y[i][j]);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   double **out;
-     }
+   double sw; /* Sum of weights */
-     printf("\n");
+   double lli; /* Individual log likelihood */
-     fprintf(ficlog,"\n");
+   int s1, s2;
-   }
+   double bbh, survp;
-   */
+   long ipmx;
+   double agexact;
-   free_matrix(a,1,npar,1,npar);
+   /*extern weight */
-   free_matrix(y,1,npar,1,npar);
+   /* We are differentiating ll according to initial status */
-   free_vector(x,1,npar);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   free_ivector(indx,1,npar);
+   /*for(i=1;i<imx;i++)
-   free_matrix(hess,1,npar,1,npar);
+     printf(" %d\n",s[4][i]);
+   */
- }
+   ++countcallfunc;
- /*************** hessian matrix ****************/
+   cov[1]=1.;
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   int i;
-   int l=1, lmax=20;
+   if(mle==1){
-   double k1,k2;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double p2[NPARMAX+1];
+       /* Computes the values of the ncovmodel covariates of the model
-   double res;
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-   double fx;
+          to be observed in j being in i according to the model.
-   int k=0,kmax=10;
+        */
-   double l1;
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+           cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   fx=func(x);
+       }
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   for(l=0 ; l <=lmax; l++){
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-     l1=pow(10,l);
+          has been calculated etc */
-     delts=delt;
+       for(mi=1; mi<= wav[i]-1; mi++){
-     for(k=1 ; k <kmax; k=k+1){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       delt = delta*(l1*k);
+           for (j=1;j<=nlstate+ndeath;j++){
-       p2[theta]=x[theta] +delt;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       k1=func(p2)-fx;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       p2[theta]=x[theta]-delt;
+           }
-       k2=func(p2)-fx;
+         for(d=0; d<dh[mi][i]; d++){
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+           newm=savm;
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
- #ifdef DEBUG
+           if(nagesqr==1)
-       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);
+             cov[3]= agexact*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);
+           for (kk=1; kk<=cptcovage;kk++) {
- #endif
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+           }
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         k=kmax;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       }
+           savm=oldm;
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+           oldm=newm;
-         k=kmax; l=lmax*10.;
+         } /* end mult */
-       }
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         delts=delt;
+         /* 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
-     }
+          * (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
-   delti[theta]=delts;
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-   return res;
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+          * probability in order to take into account the bias as a fraction of the way
- }
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+          * -stepm/2 to stepm/2 .
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+          * For stepm=1 the results are the same as for previous versions of Imach.
- {
+          * For stepm > 1 the results are less biased than in previous versions.
-   int i;
+          */
-   int l=1, l1, lmax=20;
+         s1=s[mw[mi][i]][i];
-   double k1,k2,k3,k4,res,fx;
+         s2=s[mw[mi+1][i]][i];
-   double p2[NPARMAX+1];
+         bbh=(double)bh[mi][i]/(double)stepm;
-   int k;
+         /* bias bh is positive if real duration
+          * is higher than the multiple of stepm and negative otherwise.
-   fx=func(x);
+          */
-   for (k=1; k<=2; k++) {
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+         if( s2 > nlstate){
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+           /* i.e. if s2 is a death state and if the date of death is known
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+              then the contribution to the likelihood is the probability to
-     k1=func(p2)-fx;
+              die between last step unit time and current  step unit time,
+              which is also equal to probability to die before dh
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+              minus probability to die before dh-stepm .
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+              In version up to 0.92 likelihood was computed
-     k2=func(p2)-fx;
+         as if date of death was unknown. Death was treated as any other
+         health state: the date of the interview describes the actual state
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         and not the date of a change in health state. The former idea was
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         to consider that at each interview the state was recorded
-     k3=func(p2)-fx;
+         (healthy, disable or death) and IMaCh was corrected; but when we
+         introduced the exact date of death then we should have modified
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         the contribution of an exact death to the likelihood. This new
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+         contribution is smaller and very dependent of the step unit
-     k4=func(p2)-fx;
+         stepm. It is no more the probability to die between last interview
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+         and month of death but the probability to survive from last
- #ifdef DEBUG
+         interview up to one month before death multiplied by the
-     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);
+         probability to die within a month. Thanks to Chris
-     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);
+         Jackson for correcting this bug.  Former versions increased
- #endif
+         mortality artificially. The bad side is that we add another loop
-   }
+         which slows down the processing. The difference can be up to 10%
-   return res;
+         lower mortality.
- }
+           */
+         /* If, at the beginning of the maximization mostly, the
- /************** Inverse of matrix **************/
+            cumulative probability or probability to be dead is
- void ludcmp(double **a, int n, int *indx, double *d)
+            constant (ie = 1) over time d, the difference is equal to
- {
+.  out[s1][3] = savm[s1][3]: probability, being at state
-   int i,imax,j,k;
+            s1 at precedent wave, to be dead a month before current
-   double big,dum,sum,temp;
+            wave is equal to probability, being at state s1 at
-   double *vv;
+            precedent wave, to be dead at mont of the current
+            wave. Then the observed probability (that this person died)
-   vv=vector(1,n);
+            is null according to current estimated parameter. In fact,
-   *d=1.0;
+            it should be very low but not zero otherwise the log go to
-   for (i=1;i<=n;i++) {
+            infinity.
-     big=0.0;
+         */
-     for (j=1;j<=n;j++)
+ /* #ifdef INFINITYORIGINAL */
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+ /* #else */
-     vv[i]=1.0/big;
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-   }
+ /*          lli=log(mytinydouble); */
-   for (j=1;j<=n;j++) {
+ /*        else */
-     for (i=1;i<j;i++) {
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-       sum=a[i][j];
+ /* #endif */
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+             lli=log(out[s1][s2] - savm[s1][s2]);
-       a[i][j]=sum;
-     }
+         } else if  (s2==-2) {
-     big=0.0;
+           for (j=1,survp=0. ; j<=nlstate; j++)
-     for (i=j;i<=n;i++) {
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       sum=a[i][j];
+           /*survp += out[s1][j]; */
-       for (k=1;k<j;k++)
+           lli= log(survp);
-         sum -= a[i][k]*a[k][j];
+         }
-       a[i][j]=sum;
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+         else if  (s2==-4) {
-         big=dum;
+           for (j=3,survp=0. ; j<=nlstate; j++)
-         imax=i;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       }
+           lli= log(survp);
-     }
+         }
-     if (j != imax) {
-       for (k=1;k<=n;k++) {
+         else if  (s2==-5) {
-         dum=a[imax][k];
+           for (j=1,survp=0. ; j<=2; j++)
-         a[imax][k]=a[j][k];
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         a[j][k]=dum;
+           lli= log(survp);
-       }
+         }
-       *d = -(*d);
-       vv[imax]=vv[j];
+         else{
-     }
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     indx[j]=imax;
+           /*  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 */
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+         }
-     if (j != n) {
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-       dum=1.0/(a[j][j]);
+         /*if(lli ==000.0)*/
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+         /*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); */
-     }
+         ipmx +=1;
-   }
+         sw += weight[i];
-   free_vector(vv,1,n);  /* Doesn't work */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- ;
+         /* if (lli < log(mytinydouble)){ */
- }
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
- void lubksb(double **a, int n, int *indx, double b[])
+         /* } */
- {
+       } /* end of wave */
-   int i,ii=0,ip,j;
+     } /* end of individual */
-   double sum;
+   }  else if(mle==2){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   for (i=1;i<=n;i++) {
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-     ip=indx[i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-     sum=b[ip];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     b[ip]=b[i];
+           for (j=1;j<=nlstate+ndeath;j++){
-     if (ii)
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     else if (sum) ii=i;
+           }
-     b[i]=sum;
+         for(d=0; d<=dh[mi][i]; d++){
-   }
+           newm=savm;
-   for (i=n;i>=1;i--) {
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     sum=b[i];
+           cov[2]=agexact;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+           if(nagesqr==1)
-     b[i]=sum/a[i][i];
+             cov[3]= agexact*agexact;
-   }
+           for (kk=1; kk<=cptcovage;kk++) {
- }
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           }
- void pstamp(FILE *fichier)
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+           savm=oldm;
- }
+           oldm=newm;
+         } /* end mult */
- /************ Frequencies ********************/
- 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[])
+         s1=s[mw[mi][i]][i];
- {  /* Some frequencies */
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   int first;
+         ipmx +=1;
-   double ***freq; /* Frequencies */
+         sw += weight[i];
-   double *pp, **prop;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+       } /* end of wave */
-   char fileresp[FILENAMELENGTH];
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-   pp=vector(1,nlstate);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   strcpy(fileresp,"p");
+       for(mi=1; mi<= wav[i]-1; mi++){
-   strcat(fileresp,fileres);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+           for (j=1;j<=nlstate+ndeath;j++){
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     exit(0);
+           }
-   }
+         for(d=0; d<dh[mi][i]; d++){
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+           newm=savm;
-   j1=0;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
-   j=cptcoveff;
+           if(nagesqr==1)
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+             cov[3]= agexact*agexact;
+           for (kk=1; kk<=cptcovage;kk++) {
-   first=1;
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           }
-   for(k1=1; k1<=j;k1++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     for(i1=1; i1<=ncodemax[k1];i1++){
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       j1++;
+           savm=oldm;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+           oldm=newm;
-         scanf("%d", i);*/
+         } /* end mult */
-       for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+         s1=s[mw[mi][i]][i];
-           for(m=iagemin; m <= iagemax+3; m++)
+         s2=s[mw[mi+1][i]][i];
-             freq[i][jk][m]=0;
+         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 */
-     for (i=1; i<=nlstate; i++)
+         ipmx +=1;
-       for(m=iagemin; m <= iagemax+3; m++)
+         sw += weight[i];
-         prop[i][m]=0;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
-       dateintsum=0;
+     } /* end of individual */
-       k2cpt=0;
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-       for (i=1; i<=imx; i++) {
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         bool=1;
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         if  (cptcovn>0) {
+       for(mi=1; mi<= wav[i]-1; mi++){
-           for (z1=1; z1<=cptcoveff; z1++)
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+           for (j=1;j<=nlstate+ndeath;j++){
-               bool=0;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         if (bool==1){
+           }
-           for(m=firstpass; m<=lastpass; m++){
+         for(d=0; d<dh[mi][i]; d++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+           newm=savm;
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+           cov[2]=agexact;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+           if(nagesqr==1)
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+             cov[3]= agexact*agexact;
-               if (m<lastpass) {
+           for (kk=1; kk<=cptcovage;kk++) {
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+           }
-               }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-                 dateintsum=dateintsum+k2;
+           savm=oldm;
-                 k2cpt++;
+           oldm=newm;
-               }
+         } /* end mult */
-               /*}*/
-           }
+         s1=s[mw[mi][i]][i];
-         }
+         s2=s[mw[mi+1][i]][i];
-       }
+         if( s2 > nlstate){
+           lli=log(out[s1][s2] - savm[s1][s2]);
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         }else{
-       pstamp(ficresp);
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       if  (cptcovn>0) {
+         }
-         fprintf(ficresp, "\n#********** Variable ");
+         ipmx +=1;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         sw += weight[i];
-         fprintf(ficresp, "**********\n#");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       }
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-       for(i=1; i<=nlstate;i++)
+       } /* end of wave */
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+     } /* end of individual */
-       fprintf(ficresp, "\n");
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for(i=iagemin; i <= iagemax+3; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         if(i==iagemax+3){
+       for(mi=1; mi<= wav[i]-1; mi++){
-           fprintf(ficlog,"Total");
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         }else{
+           for (j=1;j<=nlstate+ndeath;j++){
-           if(first==1){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             first=0;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-             printf("See log file for details...\n");
+           }
-           }
+         for(d=0; d<dh[mi][i]; d++){
-           fprintf(ficlog,"Age %d", i);
+           newm=savm;
-         }
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         for(jk=1; jk <=nlstate ; jk++){
+           cov[2]=agexact;
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+           if(nagesqr==1)
-             pp[jk] += freq[jk][m][i];
+             cov[3]= agexact*agexact;
-         }
+           for (kk=1; kk<=cptcovage;kk++) {
-         for(jk=1; jk <=nlstate ; jk++){
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-           for(m=-1, pos=0; m <=0 ; m++)
+           }
-             pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-             if(first==1){
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           savm=oldm;
-             }
+           oldm=newm;
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         } /* end mult */
-           }else{
-             if(first==1)
+         s1=s[mw[mi][i]][i];
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         s2=s[mw[mi+1][i]][i];
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-           }
+         ipmx +=1;
-         }
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         for(jk=1; jk <=nlstate ; jk++){
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+       } /* end of wave */
-             pp[jk] += freq[jk][m][i];
+     } /* end of individual */
-         }
+   } /* End of if */
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-           pos += pp[jk];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-           posprop += prop[jk][i];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-         }
+   return -l;
-         for(jk=1; jk <=nlstate ; jk++){
+ }
-           if(pos>=1.e-5){
-             if(first==1)
+ /*************** log-likelihood *************/
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ double funcone( double *x)
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ {
-           }else{
+   /* Same as likeli but slower because of a lot of printf and if */
-             if(first==1)
+   int i, ii, j, k, mi, d, kk;
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double **out;
-           }
+   double lli; /* Individual log likelihood */
-           if( i <= iagemax){
+   double llt;
-             if(pos>=1.e-5){
+   int s1, s2;
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   double bbh, survp;
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+   double agexact;
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+   /*extern weight */
-             }
+   /* We are differentiating ll according to initial status */
-             else
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   /*for(i=1;i<imx;i++)
-           }
+     printf(" %d\n",s[4][i]);
-         }
+   */
+   cov[1]=1.;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
-           for(m=-1; m <=nlstate+ndeath; m++)
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+     for(mi=1; mi<= wav[i]-1; mi++){
-             }
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-         if(i <= iagemax)
+         for (j=1;j<=nlstate+ndeath;j++){
-           fprintf(ficresp,"\n");
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         if(first==1)
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           printf("Others in log...\n");
+         }
-         fprintf(ficlog,"\n");
+       for(d=0; d<dh[mi][i]; d++){
-       }
+         newm=savm;
-     }
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   }
+         cov[2]=agexact;
-   dateintmean=dateintsum/k2cpt;
+         if(nagesqr==1)
+           cov[3]= agexact*agexact;
-   fclose(ficresp);
+         for (kk=1; kk<=cptcovage;kk++) {
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-   free_vector(pp,1,nlstate);
+         }
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-   /* End of Freq */
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
- }
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- /************ Prevalence ********************/
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
- 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)
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
- {
+         savm=oldm;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+         oldm=newm;
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       } /* end mult */
-      We still use firstpass and lastpass as another selection.
-   */
+       s1=s[mw[mi][i]][i];
+       s2=s[mw[mi+1][i]][i];
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+       bbh=(double)bh[mi][i]/(double)stepm;
-   double ***freq; /* Frequencies */
+       /* bias is positive if real duration
-   double *pp, **prop;
+        * is higher than the multiple of stepm and negative otherwise.
-   double pos,posprop;
+        */
-   double  y2; /* in fractional years */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-   int iagemin, iagemax;
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
-   iagemin= (int) agemin;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   iagemax= (int) agemax;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   /*pp=vector(1,nlstate);*/
+         lli= log(survp);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       }else if (mle==1){
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   j1=0;
+       } else if(mle==2){
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   j=cptcoveff;
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   if (cptcovn<1) {j=1;ncodemax[1]=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 */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   for(k1=1; k1<=j;k1++){
+         lli=log(out[s1][s2]); /* Original formula */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+       } else{  /* mle=0 back to 1 */
-       j1++;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-       for (i=1; i<=nlstate; i++)
+       } /* End of if */
-         for(m=iagemin; m <= iagemax+3; m++)
+       ipmx +=1;
-           prop[i][m]=0.0;
+       sw += weight[i];
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       for (i=1; i<=imx; i++) { /* Each individual */
+       /*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]); */
-         bool=1;
+       if(globpr){
-         if  (cptcovn>0) {
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-           for (z1=1; z1<=cptcoveff; z1++)
+  %11.6f %11.6f %11.6f ", \
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-               bool=0;
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-         }
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-         if (bool==1) {
+           llt +=ll[k]*gipmx/gsw;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+         }
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+         fprintf(ficresilk," %10.6f\n", -llt);
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+       }
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     } /* end of wave */
-               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);
+   } /* end of individual */
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   if(globpr==0){ /* First time we count the contributions and weights */
-               }
+     gipmx=ipmx;
-             }
+     gsw=sw;
-           } /* end selection of waves */
+   }
-         }
+   return -l;
-       }
+ }
-       for(i=iagemin; i <= iagemax+3; i++){
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+ /*************** function likelione ***********/
-           posprop += prop[jk][i];
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-         }
+ {
+   /* This routine should help understanding what is done with
-         for(jk=1; jk <=nlstate ; jk++){
+      the selection of individuals/waves and
-           if( i <=  iagemax){
+      to check the exact contribution to the likelihood.
-             if(posprop>=1.e-5){
+      Plotting could be done.
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+    */
-             }
+   int k;
-           }
-         }/* end jk */
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-       }/* end i */
+     strcpy(fileresilk,"ilk");
-     } /* end i1 */
+     strcat(fileresilk,fileres);
-   } /* end k1 */
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   /*free_vector(pp,1,nlstate);*/
+     }
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+     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");
- }  /* End of prevalence */
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
- /************* Waves Concatenation ***************/
+     for(k=1; k<=nlstate; k++)
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
- 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(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
- {
+   }
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-      Death is a valid wave (if date is known).
+   *fretone=(*funcone)(p);
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+   if(*globpri !=0){
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+     fclose(ficresilk);
-      and mw[mi+1][i]. dh depends on stepm.
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-      */
+     fflush(fichtm);
+   }
-   int i, mi, m;
+   return;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+ }
-      double sum=0., jmean=0.;*/
-   int first;
-   int j, k=0,jk, ju, jl;
+ /*********** Maximum Likelihood Estimation ***************/
-   double sum=0.;
-   first=0;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   jmin=1e+5;
+ {
-   jmax=-1;
+   int i,j, iter=0;
-   jmean=0.;
+   double **xi;
-   for(i=1; i<=imx; i++){
+   double fret;
-     mi=0;
+   double fretone; /* Only one call to likelihood */
-     m=firstpass;
+   /*  char filerespow[FILENAMELENGTH];*/
-     while(s[m][i] <= nlstate){
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+ #ifdef NLOPT
-         mw[++mi][i]=m;
+   int creturn;
-       if(m >=lastpass)
+   nlopt_opt opt;
-         break;
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-       else
+   double *lb;
-         m++;
+   double minf; /* the minimum objective value, upon return */
-     }/* end while */
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-     if (s[m][i] > nlstate){
+   myfunc_data dinst, *d = &dinst;
-       mi++;     /* Death is another wave */
+ #endif
-       /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
-       mw[mi][i]=m;
+   xi=matrix(1,npar,1,npar);
-     }
+   for (i=1;i<=npar;i++)
+     for (j=1;j<=npar;j++)
-     wav[i]=mi;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     if(mi==0){
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-       nbwarn++;
+   strcpy(filerespow,"pow");
-       if(first==0){
+   strcat(filerespow,fileres);
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-         first=1;
+     printf("Problem with resultfile: %s\n", filerespow);
-       }
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       if(first==1){
+   }
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-       }
+   for (i=1;i<=nlstate;i++)
-     } /* end mi==0 */
+     for(j=1;j<=nlstate+ndeath;j++)
-   } /* End individuals */
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   fprintf(ficrespow,"\n");
-   for(i=1; i<=imx; i++){
+ #ifdef POWELL
-     for(mi=1; mi<wav[i];mi++){
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-       if (stepm <=0)
+ #endif
-         dh[mi][i]=1;
-       else{
+ #ifdef NLOPT
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+ #ifdef NEWUOA
-           if (agedc[i] < 2*AGESUP) {
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+ #else
-             if(j==0) j=1;  /* Survives at least one month after exam */
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-             else if(j<0){
+ #endif
-               nberr++;
+   lb=vector(0,npar-1);
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-               j=1; /* Temporary Dangerous patch */
+   nlopt_set_lower_bounds(opt, lb);
-               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);
+   nlopt_set_initial_step1(opt, 0.1);
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-             }
+   d->function = func;
-             k=k+1;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-             if (j >= jmax){
+   nlopt_set_min_objective(opt, myfunc, d);
-               jmax=j;
+   nlopt_set_xtol_rel(opt, ftol);
-               ijmax=i;
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-             }
+     printf("nlopt failed! %d\n",creturn);
-             if (j <= jmin){
+   }
-               jmin=j;
+   else {
-               ijmin=i;
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-             }
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-             sum=sum+j;
+     iter=1; /* not equal */
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   }
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   nlopt_destroy(opt);
-           }
+ #endif
-         }
+   free_matrix(xi,1,npar,1,npar);
-         else{
+   fclose(ficrespow);
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
- /*        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]); */
+   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-           k=k+1;
-           if (j >= jmax) {
+ }
-             jmax=j;
-             ijmax=i;
+ /**** Computes Hessian and covariance matrix ***/
-           }
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-           else if (j <= jmin){
+ {
-             jmin=j;
+   double  **a,**y,*x,pd;
-             ijmin=i;
+   double **hess;
-           }
+   int i, j;
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   int *indx;
-           /*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){
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-             nberr++;
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-             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]);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-             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]);
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-           }
+   double gompertz(double p[]);
-           sum=sum+j;
+   hess=matrix(1,npar,1,npar);
-         }
-         jk= j/stepm;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-         jl= j -jk*stepm;
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-         ju= j -(jk+1)*stepm;
+   for (i=1;i<=npar;i++){
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+     printf("%d",i);fflush(stdout);
-           if(jl==0){
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-             dh[mi][i]=jk;
-             bh[mi][i]=0;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-           }else{ /* We want a negative bias in order to only have interpolation ie
-                   * at the price of an extra matrix product in likelihood */
+     /*  printf(" %f ",p[i]);
-             dh[mi][i]=jk+1;
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-             bh[mi][i]=ju;
+   }
-           }
-         }else{
+   for (i=1;i<=npar;i++) {
-           if(jl <= -ju){
+     for (j=1;j<=npar;j++)  {
-             dh[mi][i]=jk;
+       if (j>i) {
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         printf(".%d%d",i,j);fflush(stdout);
-                                  * is higher than the multiple of stepm and negative otherwise.
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-                                  */
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-           }
-           else{
+         hess[j][i]=hess[i][j];
-             dh[mi][i]=jk+1;
+         /*printf(" %lf ",hess[i][j]);*/
-             bh[mi][i]=ju;
+       }
-           }
+     }
-           if(dh[mi][i]==0){
+   }
-             dh[mi][i]=1; /* At least one step */
+   printf("\n");
-             bh[mi][i]=ju; /* At least one step */
+   fprintf(ficlog,"\n");
-             /*  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);*/
-           }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-         } /* end if mle */
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       }
-     } /* end wave */
+   a=matrix(1,npar,1,npar);
-   }
+   y=matrix(1,npar,1,npar);
-   jmean=sum/k;
+   x=vector(1,npar);
-   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);
+   indx=ivector(1,npar);
-   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 (i=1;i<=npar;i++)
-  }
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+   ludcmp(a,npar,indx,&pd);
- /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx)
+   for (j=1;j<=npar;j++) {
- {
+     for (i=1;i<=npar;i++) x[i]=0;
+     x[j]=1;
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+     lubksb(a,npar,indx,x);
-   int cptcode=0;
+     for (i=1;i<=npar;i++){
-   cptcoveff=0;
+       matcov[i][j]=x[i];
+     }
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   }
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   printf("\n#Hessian matrix#\n");
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   for (i=1;i<=npar;i++) {
-                                modality*/
+     for (j=1;j<=npar;j++) {
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       printf("%.3e ",hess[i][j]);
-       Ndum[ij]++; /*store the modality */
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+     }
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+     printf("\n");
-                                        Tvar[j]. If V=sex and male is 0 and
+     fprintf(ficlog,"\n");
-                                        female is 1, then  cptcode=1.*/
+   }
-     }
+   /* Recompute Inverse */
-     for (i=0; i<=cptcode; i++) {
+   for (i=1;i<=npar;i++)
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-     }
+   ludcmp(a,npar,indx,&pd);
-     ij=1;
+   /*  printf("\n#Hessian matrix recomputed#\n");
-     for (i=1; i<=ncodemax[j]; i++) {
-       for (k=0; k<= maxncov; k++) {
+   for (j=1;j<=npar;j++) {
-         if (Ndum[k] != 0) {
+     for (i=1;i<=npar;i++) x[i]=0;
-           nbcode[Tvar[j]][ij]=k;
+     x[j]=1;
-           /* 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; */
+     lubksb(a,npar,indx,x);
+     for (i=1;i<=npar;i++){
-           ij++;
+       y[i][j]=x[i];
-         }
+       printf("%.3e ",y[i][j]);
-         if (ij > ncodemax[j]) break;
+       fprintf(ficlog,"%.3e ",y[i][j]);
-       }
+     }
-     }
+     printf("\n");
-   }
+     fprintf(ficlog,"\n");
+   }
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   */
-  for (i=1; i<=ncovmodel-2; i++) {
+   free_matrix(a,1,npar,1,npar);
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+   free_matrix(y,1,npar,1,npar);
-    ij=Tvar[i];
+   free_vector(x,1,npar);
-    Ndum[ij]++;
+   free_ivector(indx,1,npar);
-  }
+   free_matrix(hess,1,npar,1,npar);
-  ij=1;
-  for (i=1; i<= maxncov; i++) {
+ }
-    if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i; /*For printing */
+ /*************** hessian matrix ****************/
-      ij++;
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-    }
+ {
-  }
+   int i;
+   int l=1, lmax=20;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+   double k1,k2;
- }
+   double p2[MAXPARM+1]; /* identical to x */
+   double res;
- /*********** Health Expectancies ****************/
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double fx;
- 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[] )
+   int k=0,kmax=10;
+   double l1;
- {
-   /* Health expectancies, no variances */
+   fx=func(x);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   double age, agelim, hf;
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   double ***p3mat;
+     l1=pow(10,l);
-   double eip;
+     delts=delt;
+     for(k=1 ; k <kmax; k=k+1){
-   pstamp(ficreseij);
+       delt = delta*(l1*k);
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+       p2[theta]=x[theta] +delt;
-   fprintf(ficreseij,"# Age");
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   for(i=1; i<=nlstate;i++){
+       p2[theta]=x[theta]-delt;
-     for(j=1; j<=nlstate;j++){
+       k2=func(p2)-fx;
-       fprintf(ficreseij," e%1d%1d ",i,j);
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-     }
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-     fprintf(ficreseij," e%1d. ",i);
-   }
+ #ifdef DEBUGHESS
-   fprintf(ficreseij,"\n");
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+ #endif
-   if(estepm < stepm){
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   }
+         k=kmax;
-   else  hstepm=estepm;
+       }
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-    * This is mainly to measure the difference between two models: for example
+         k=kmax; l=lmax*10;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+       }
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-    * progression in between and thus overestimating or underestimating according
+         delts=delt;
-    * to the curvature of the survival function. If, for the same date, we
+       }
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+     }
-    * to compare the new estimate of Life expectancy with the same linear
+   }
-    * hypothesis. A more precise result, taking into account a more precise
+   delti[theta]=delts;
-    * curvature will be obtained if estepm is as small as stepm. */
+   return res;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+ }
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int 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
+   int i;
-      and note for a fixed period like estepm months */
+   int l=1, lmax=20;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   double k1,k2,k3,k4,res,fx;
-      survival function given by stepm (the optimization length). Unfortunately it
+   double p2[MAXPARM+1];
-      means that if the survival funtion is printed only each two years of age and if
+   int k;
-      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.
+   fx=func(x);
-   */
+   for (k=1; k<=2; k++) {
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     for (i=1;i<=npar;i++) p2[i]=x[i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   agelim=AGESUP;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-   /* If stepm=6 months */
+     k1=func(p2)-fx;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
- /* nhstepm age range expressed in number of stepm */
+     k2=func(p2)-fx;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-   /* if (stepm >= YEARM) hstepm=1;*/
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     k3=func(p2)-fx;
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-   for (age=bage; age<=fage; age ++){
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     k4=func(p2)-fx;
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+ #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);
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     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
-     printf("%d|",(int)age);fflush(stdout);
+   }
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   return res;
+ }
-     /* Computing expectancies */
+ /************** Inverse of matrix **************/
-     for(i=1; i<=nlstate;i++)
+ void ludcmp(double **a, int n, int *indx, double *d)
-       for(j=1; j<=nlstate;j++)
+ {
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   int i,imax,j,k;
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+   double big,dum,sum,temp;
+   double *vv;
-           /*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]);*/
+   vv=vector(1,n);
-         }
+   *d=1.0;
+   for (i=1;i<=n;i++) {
-     fprintf(ficreseij,"%3.0f",age );
+     big=0.0;
-     for(i=1; i<=nlstate;i++){
+     for (j=1;j<=n;j++)
-       eip=0;
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-       for(j=1; j<=nlstate;j++){
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-         eip +=eij[i][j][(int)age];
+     vv[i]=1.0/big;
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+   }
-       }
+   for (j=1;j<=n;j++) {
-       fprintf(ficreseij,"%9.4f", eip );
+     for (i=1;i<j;i++) {
-     }
+       sum=a[i][j];
-     fprintf(ficreseij,"\n");
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+       a[i][j]=sum;
-   }
+     }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     big=0.0;
-   printf("\n");
+     for (i=j;i<=n;i++) {
-   fprintf(ficlog,"\n");
+       sum=a[i][j];
+       for (k=1;k<j;k++)
- }
+         sum -= a[i][k]*a[k][j];
+       a[i][j]=sum;
- 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[] )
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
+         big=dum;
- {
+         imax=i;
-   /* Covariances of health expectancies eij and of total life expectancies according
+       }
-    to initial status i, ei. .
+     }
-   */
+     if (j != imax) {
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+       for (k=1;k<=n;k++) {
-   double age, agelim, hf;
+         dum=a[imax][k];
-   double ***p3matp, ***p3matm, ***varhe;
+         a[imax][k]=a[j][k];
-   double **dnewm,**doldm;
+         a[j][k]=dum;
-   double *xp, *xm;
+       }
-   double **gp, **gm;
+       *d = -(*d);
-   double ***gradg, ***trgradg;
+       vv[imax]=vv[j];
-   int theta;
+     }
+     indx[j]=imax;
-   double eip, vip;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
+     if (j != n) {
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+       dum=1.0/(a[j][j]);
-   xp=vector(1,npar);
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   xm=vector(1,npar);
+     }
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   }
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   free_vector(vv,1,n);  /* Doesn't work */
+ ;
-   pstamp(ficresstdeij);
+ }
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   fprintf(ficresstdeij,"# Age");
+ void lubksb(double **a, int n, int *indx, double b[])
-   for(i=1; i<=nlstate;i++){
+ {
-     for(j=1; j<=nlstate;j++)
+   int i,ii=0,ip,j;
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   double sum;
-     fprintf(ficresstdeij," e%1d. ",i);
-   }
+   for (i=1;i<=n;i++) {
-   fprintf(ficresstdeij,"\n");
+     ip=indx[i];
+     sum=b[ip];
-   pstamp(ficrescveij);
+     b[ip]=b[i];
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+     if (ii)
-   fprintf(ficrescveij,"# Age");
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   for(i=1; i<=nlstate;i++)
+     else if (sum) ii=i;
-     for(j=1; j<=nlstate;j++){
+     b[i]=sum;
-       cptj= (j-1)*nlstate+i;
+   }
-       for(i2=1; i2<=nlstate;i2++)
+   for (i=n;i>=1;i--) {
-         for(j2=1; j2<=nlstate;j2++){
+     sum=b[i];
-           cptj2= (j2-1)*nlstate+i2;
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-           if(cptj2 <= cptj)
+     b[i]=sum/a[i][i];
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+   }
-         }
+ }
-     }
-   fprintf(ficrescveij,"\n");
+ void pstamp(FILE *fichier)
+ {
-   if(estepm < stepm){
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
-   }
-   else  hstepm=estepm;
+ /************ Frequencies ********************/
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+ 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[])
-    * This is mainly to measure the difference between two models: for example
+ {  /* Some frequencies */
-    * 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
+   int i, m, jk, j1, bool, z1,j;
-    * progression in between and thus overestimating or underestimating according
+   int first;
-    * to the curvature of the survival function. If, for the same date, we
+   double ***freq; /* Frequencies */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   double *pp, **prop;
-    * to compare the new estimate of Life expectancy with the same linear
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-    * hypothesis. A more precise result, taking into account a more precise
+   char fileresp[FILENAMELENGTH];
-    * curvature will be obtained if estepm is as small as stepm. */
+   pp=vector(1,nlstate);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   strcpy(fileresp,"p");
-      nhstepm is the number of hstepm from age to agelim
+   strcat(fileresp,fileres);
-      nstepm is the number of stepm from age to agelin.
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-      Look at hpijx to understand the reason of that which relies in memory size
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-      and note for a fixed period like estepm months */
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     exit(0);
-      survival function given by stepm (the optimization length). Unfortunately it
+   }
-      means that if the survival funtion is printed only each two years of age and if
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   j1=0;
-      results. So we changed our mind and took the option of the best precision.
-   */
+   j=cptcoveff;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   /* If stepm=6 months */
+   first=1;
-   /* nhstepm age range expressed in number of stepm */
-   agelim=AGESUP;
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /*    j1++; */
-   /* if (stepm >= YEARM) hstepm=1;*/
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         scanf("%d", i);*/
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (i=-5; i<=nlstate+ndeath; i++)
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+           for(m=iagemin; m <= iagemax+3; m++)
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+             freq[i][jk][m]=0;
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+       for (i=1; i<=nlstate; i++)
+         for(m=iagemin; m <= iagemax+3; m++)
-   for (age=bage; age<=fage; age ++){
+           prop[i][m]=0;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       dateintsum=0;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       k2cpt=0;
+       for (i=1; i<=imx; i++) {
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+         bool=1;
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-     /* Computing  Variances of health expectancies */
+           for (z1=1; z1<=cptcoveff; z1++)
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-        decrease memory allocation */
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-     for(theta=1; theta <=npar; theta++){
+               bool=0;
-       for(i=1; i<=npar; i++){
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-       }
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=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++){
+         if (bool==1){
-         for(i=1; i<=nlstate; i++){
+           for(m=firstpass; m<=lastpass; m++){
-           for(h=0; h<=nhstepm-1; h++){
+             k2=anint[m][i]+(mint[m][i]/12.);
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-           }
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-         }
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-       }
+               if (m<lastpass) {
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-         for(h=0; h<=nhstepm-1; h++){
+               }
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         }
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-     }/* End theta */
+                 dateintsum=dateintsum+k2;
+                 k2cpt++;
+               }
-     for(h=0; h<=nhstepm-1; h++)
+               /*}*/
-       for(j=1; j<=nlstate*nlstate;j++)
+           }
-         for(theta=1; theta <=npar; theta++)
+         }
-           trgradg[h][j][theta]=gradg[h][theta][j];
+       } /* end i */
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+       pstamp(ficresp);
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+       if  (cptcovn>0) {
-         varhe[ij][ji][(int)age] =0.;
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      printf("%d|",(int)age);fflush(stdout);
+         fprintf(ficresp, "**********\n#");
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+         fprintf(ficlog, "\n#********** Variable ");
-      for(h=0;h<=nhstepm-1;h++){
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       for(k=0;k<=nhstepm-1;k++){
+         fprintf(ficlog, "**********\n#");
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+       }
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+       for(i=1; i<=nlstate;i++)
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+       fprintf(ficresp, "\n");
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-       }
+       for(i=iagemin; i <= iagemax+3; i++){
-     }
+         if(i==iagemax+3){
+           fprintf(ficlog,"Total");
-     /* Computing expectancies */
+         }else{
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+           if(first==1){
-     for(i=1; i<=nlstate;i++)
+             first=0;
-       for(j=1; j<=nlstate;j++)
+             printf("See log file for details...\n");
-         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;
+           fprintf(ficlog,"Age %d", i);
+         }
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-         }
+             pp[jk] += freq[jk][m][i];
+         }
-     fprintf(ficresstdeij,"%3.0f",age );
+         for(jk=1; jk <=nlstate ; jk++){
-     for(i=1; i<=nlstate;i++){
+           for(m=-1, pos=0; m <=0 ; m++)
-       eip=0.;
+             pos += freq[jk][m][i];
-       vip=0.;
+           if(pp[jk]>=1.e-10){
-       for(j=1; j<=nlstate;j++){
+             if(first==1){
-         eip += eij[i][j][(int)age];
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+             }
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+           }else{
-       }
+             if(first==1)
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     }
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     fprintf(ficresstdeij,"\n");
+           }
+         }
-     fprintf(ficrescveij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++)
+         for(jk=1; jk <=nlstate ; jk++){
-       for(j=1; j<=nlstate;j++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-         cptj= (j-1)*nlstate+i;
+             pp[jk] += freq[jk][m][i];
-         for(i2=1; i2<=nlstate;i2++)
+         }
-           for(j2=1; j2<=nlstate;j2++){
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-             cptj2= (j2-1)*nlstate+i2;
+           pos += pp[jk];
-             if(cptj2 <= cptj)
+           posprop += prop[jk][i];
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+         }
-           }
+         for(jk=1; jk <=nlstate ; jk++){
-       }
+           if(pos>=1.e-5){
-     fprintf(ficrescveij,"\n");
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   }
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+           }else{
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+             if(first==1)
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           }
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           if( i <= iagemax){
-   printf("\n");
+             if(pos>=1.e-5){
-   fprintf(ficlog,"\n");
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   free_vector(xm,1,npar);
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   free_vector(xp,1,npar);
+             }
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+             else
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+           }
- }
+         }
- /************ Variance ******************/
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+           for(m=-1; m <=nlstate+ndeath; m++)
- {
+             if(freq[jk][m][i] !=0 ) {
-   /* Variance of health expectancies */
+             if(first==1)
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   /* double **newm;*/
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   double **dnewm,**doldm;
+             }
-   double **dnewmp,**doldmp;
+         if(i <= iagemax)
-   int i, j, nhstepm, hstepm, h, nstepm ;
+           fprintf(ficresp,"\n");
-   int k, cptcode;
+         if(first==1)
-   double *xp;
+           printf("Others in log...\n");
-   double **gp, **gm;  /* for var eij */
+         fprintf(ficlog,"\n");
-   double ***gradg, ***trgradg; /*for var eij */
+       }
-   double **gradgp, **trgradgp; /* for var p point j */
+       /*}*/
-   double *gpp, *gmp; /* for var p point j */
+   }
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   dateintmean=dateintsum/k2cpt;
-   double ***p3mat;
-   double age,agelim, hf;
+   fclose(ficresp);
-   double ***mobaverage;
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   int theta;
+   free_vector(pp,1,nlstate);
-   char digit[4];
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-   char digitp[25];
+   /* End of Freq */
+ }
-   char fileresprobmorprev[FILENAMELENGTH];
+ /************ Prevalence ********************/
-   if(popbased==1){
+ 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)
-     if(mobilav!=0)
+ {
-       strcpy(digitp,"-populbased-mobilav-");
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-     else strcpy(digitp,"-populbased-nomobil-");
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-   }
+      We still use firstpass and lastpass as another selection.
-   else
+   */
-     strcpy(digitp,"-stablbased-");
+   int i, m, jk, j1, bool, z1,j;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double **prop;
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   double posprop;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   double  y2; /* in fractional years */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   int iagemin, iagemax;
-     }
+   int first; /** to stop verbosity which is redirected to log file */
-   }
+   iagemin= (int) agemin;
-   strcpy(fileresprobmorprev,"prmorprev");
+   iagemax= (int) agemax;
-   sprintf(digit,"%-d",ij);
+   /*pp=vector(1,nlstate);*/
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   j1=0;
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   /*j=cptcoveff;*/
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+   first=1;
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+       j1++;*/
-   pstamp(ficresprobmorprev);
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+       for (i=1; i<=nlstate; i++)
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+         for(m=iagemin; m <= iagemax+3; m++)
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+           prop[i][m]=0.0;
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
+       for (i=1; i<=imx; i++) { /* Each individual */
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+         bool=1;
-   }
+         if  (cptcovn>0) {
-   fprintf(ficresprobmorprev,"\n");
+           for (z1=1; z1<=cptcoveff; z1++)
-   fprintf(ficgp,"\n# Routine varevsij");
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+               bool=0;
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+         }
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+         if (bool==1) {
- /*   } */
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   pstamp(ficresvij);
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-   if(popbased==1)
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+               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);
-   else
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-   fprintf(ficresvij,"# Age");
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-   for(i=1; i<=nlstate;i++)
+                 prop[s[m][i]][iagemax+3] += weight[i];
-     for(j=1; j<=nlstate;j++)
+               }
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+             }
-   fprintf(ficresvij,"\n");
+           } /* end selection of waves */
+         }
-   xp=vector(1,npar);
+       }
-   dnewm=matrix(1,nlstate,1,npar);
+       for(i=iagemin; i <= iagemax+3; i++){
-   doldm=matrix(1,nlstate,1,nlstate);
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+           posprop += prop[jk][i];
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         }
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+         for(jk=1; jk <=nlstate ; jk++){
-   gpp=vector(nlstate+1,nlstate+ndeath);
+           if( i <=  iagemax){
-   gmp=vector(nlstate+1,nlstate+ndeath);
+             if(posprop>=1.e-5){
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+               probs[i][jk][j1]= prop[jk][i]/posprop;
+             } else{
-   if(estepm < stepm){
+               if(first==1){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+                 first=0;
-   }
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-   else  hstepm=estepm;
+               }
-   /* For example we decided to compute the life expectancy with the smallest unit */
+             }
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+           }
-      nhstepm is the number of hstepm from age to agelim
+         }/* end jk */
-      nstepm is the number of stepm from age to agelin.
+       }/* end i */
-      Look at hpijx to understand the reason of that which relies in memory size
+     /*} *//* end i1 */
-      and note for a fixed period like k years */
+   } /* end j1 */
-   /* 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
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-      means that if the survival funtion is printed every two years of age and if
+   /*free_vector(pp,1,nlstate);*/
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-      results. So we changed our mind and took the option of the best precision.
+ }  /* End of prevalence */
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ /************* Waves Concatenation ***************/
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ 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)
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ {
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      Death is a valid wave (if date is known).
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-     gp=matrix(0,nhstepm,1,nlstate);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-     gm=matrix(0,nhstepm,1,nlstate);
+      and mw[mi+1][i]. dh depends on stepm.
+      */
-     for(theta=1; theta <=npar; theta++){
+   int i, mi, m;
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+      double sum=0., jmean=0.;*/
-       }
+   int first;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   int j, k=0,jk, ju, jl;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   double sum=0.;
+   first=0;
-       if (popbased==1) {
+   jmin=100000;
-         if(mobilav ==0){
+   jmax=-1;
-           for(i=1; i<=nlstate;i++)
+   jmean=0.;
-             prlim[i][i]=probs[(int)age][i][ij];
+   for(i=1; i<=imx; i++){
-         }else{ /* mobilav */
+     mi=0;
-           for(i=1; i<=nlstate;i++)
+     m=firstpass;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     while(s[m][i] <= nlstate){
-         }
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-       }
+         mw[++mi][i]=m;
+       if(m >=lastpass)
-       for(j=1; j<= nlstate; j++){
+         break;
-         for(h=0; h<=nhstepm; h++){
+       else
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+         m++;
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+     }/* end while */
-         }
+     if (s[m][i] > nlstate){
-       }
+       mi++;     /* Death is another wave */
-       /* This for computing probability of death (h=1 means
+       /* if(mi==0)  never been interviewed correctly before death */
-          computed over hstepm matrices product = hstepm*stepm months)
+          /* Only death is a correct wave */
-          as a weighted average of prlim.
+       mw[mi][i]=m;
-       */
+     }
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+     wav[i]=mi;
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+     if(mi==0){
-       }
+       nbwarn++;
-       /* end probability of death */
+       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);
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+         first=1;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       if(first==1){
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       }
-       if (popbased==1) {
+     } /* end mi==0 */
-         if(mobilav ==0){
+   } /* End individuals */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+   for(i=1; i<=imx; i++){
-         }else{ /* mobilav */
+     for(mi=1; mi<wav[i];mi++){
-           for(i=1; i<=nlstate;i++)
+       if (stepm <=0)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+         dh[mi][i]=1;
-         }
+       else{
-       }
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+           if (agedc[i] < 2*AGESUP) {
-       for(j=1; j<= nlstate; j++){
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-         for(h=0; h<=nhstepm; h++){
+             if(j==0) j=1;  /* Survives at least one month after exam */
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+             else if(j<0){
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+               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]);
-       }
+               j=1; /* Temporary Dangerous patch */
-       /* This for computing probability of death (h=1 means
+               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);
-          computed over hstepm matrices product = hstepm*stepm months)
+               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]);
-          as a weighted average of prlim.
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-       */
+             }
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+             k=k+1;
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+             if (j >= jmax){
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+               jmax=j;
-       }
+               ijmax=i;
-       /* end probability of death */
+             }
+             if (j <= jmin){
-       for(j=1; j<= nlstate; j++) /* vareij */
+               jmin=j;
-         for(h=0; h<=nhstepm; h++){
+               ijmin=i;
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+             }
-         }
+             sum=sum+j;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+           }
-       }
+         }
+         else{
-     } /* End theta */
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+           k=k+1;
-     for(h=0; h<=nhstepm; h++) /* veij */
+           if (j >= jmax) {
-       for(j=1; j<=nlstate;j++)
+             jmax=j;
-         for(theta=1; theta <=npar; theta++)
+             ijmax=i;
-           trgradg[h][j][theta]=gradg[h][theta][j];
+           }
+           else if (j <= jmin){
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+             jmin=j;
-       for(theta=1; theta <=npar; theta++)
+             ijmin=i;
-         trgradgp[j][theta]=gradgp[theta][j];
+           }
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           if(j<0){
-     for(i=1;i<=nlstate;i++)
+             nberr++;
-       for(j=1;j<=nlstate;j++)
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         vareij[i][j][(int)age] =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(h=0;h<=nhstepm;h++){
+           sum=sum+j;
-       for(k=0;k<=nhstepm;k++){
+         }
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         jk= j/stepm;
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+         jl= j -jk*stepm;
-         for(i=1;i<=nlstate;i++)
+         ju= j -(jk+1)*stepm;
-           for(j=1;j<=nlstate;j++)
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+           if(jl==0){
-       }
+             dh[mi][i]=jk;
-     }
+             bh[mi][i]=0;
+           }else{ /* We want a negative bias in order to only have interpolation ie
-     /* pptj */
+                   * to avoid the price of an extra matrix product in likelihood */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+             dh[mi][i]=jk+1;
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+             bh[mi][i]=ju;
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+           }
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         }else{
-         varppt[j][i]=doldmp[j][i];
+           if(jl <= -ju){
-     /* end ppptj */
+             dh[mi][i]=jk;
-     /*  x centered again */
+             bh[mi][i]=jl;       /* bias is positive if real duration
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+                                  * is higher than the multiple of stepm and negative otherwise.
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+                                  */
+           }
-     if (popbased==1) {
+           else{
-       if(mobilav ==0){
+             dh[mi][i]=jk+1;
-         for(i=1; i<=nlstate;i++)
+             bh[mi][i]=ju;
-           prlim[i][i]=probs[(int)age][i][ij];
+           }
-       }else{ /* mobilav */
+           if(dh[mi][i]==0){
-         for(i=1; i<=nlstate;i++)
+             dh[mi][i]=1; /* At least one step */
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+             bh[mi][i]=ju; /* At least one step */
-       }
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-     }
+           }
+         } /* end if mle */
-     /* This for computing probability of death (h=1 means
+       }
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+     } /* end wave */
-        as a weighted average of prlim.
+   }
-     */
+   jmean=sum/k;
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   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);
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   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);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+  }
-     }
-     /* end probability of death */
+ /*********** Tricode ****************************/
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+ {
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-       for(i=1; i<=nlstate;i++){
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-       }
+    * nbcode[Tvar[j]][1]=
-     }
+   */
-     fprintf(ficresprobmorprev,"\n");
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-     fprintf(ficresvij,"%.0f ",age );
+   int modmaxcovj=0; /* Modality max of covariates j */
-     for(i=1; i<=nlstate;i++)
+   int cptcode=0; /* Modality max of covariates j */
-       for(j=1; j<=nlstate;j++){
+   int modmincovj=0; /* Modality min of covariates j */
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-       }
-     fprintf(ficresvij,"\n");
+   cptcoveff=0;
-     free_matrix(gp,0,nhstepm,1,nlstate);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   /* Loop on covariates without age and products */
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
-   } /* End age */
+     for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+                                modality of this covariate Vj*/
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+                                     * If product of Vn*Vm, still boolean *:
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+                                       modality of the nth covariate of individual i. */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       if (ij > modmaxcovj)
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+         modmaxcovj=ij;
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+       else if (ij < modmincovj)
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+         modmincovj=ij;
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+       if ((ij < -1) && (ij > NCOVMAX)){
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   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);
+         exit(1);
-   /*  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);
+       }else
- */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       /* getting the maximum value of the modality of the covariate
-   free_vector(xp,1,npar);
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   free_matrix(doldm,1,nlstate,1,nlstate);
+          female is 1, then modmaxcovj=1.*/
-   free_matrix(dnewm,1,nlstate,1,npar);
+     } /* end for loop on individuals i */
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     cptcode=modmaxcovj;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   fclose(ficresprobmorprev);
+    /*for (i=0; i<=cptcode; i++) {*/
-   fflush(ficgp);
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-   fflush(fichtm);
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
- }  /* end varevsij */
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
- /************ Variance of prevlim ******************/
+         if( k != -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[])
+           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
- {
+                              covariate for which somebody answered excluding
-   /* Variance of prevalence limit */
+                              undefined. Usually 2: 0 and 1. */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+         }
-   double **newm;
+         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
-   double **dnewm,**doldm;
+                              covariate for which somebody answered including
-   int i, j, nhstepm, hstepm;
+                              undefined. Usually 3: -1, 0 and 1. */
-   int k, cptcode;
+       }
-   double *xp;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   double *gp, *gm;
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   double **gradg, **trgradg;
+     } /* Ndum[-1] number of undefined modalities */
-   double age,agelim;
-   int theta;
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-   pstamp(ficresvpl);
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+        modmincovj=3; modmaxcovj = 7;
-   fprintf(ficresvpl,"# Age");
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-   for(i=1; i<=nlstate;i++)
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-       fprintf(ficresvpl," %1d-%1d",i,i);
+        defining two dummy variables: variables V1_1 and V1_2.
-   fprintf(ficresvpl,"\n");
+        nbcode[Tvar[j]][ij]=k;
+        nbcode[Tvar[j]][1]=0;
-   xp=vector(1,npar);
+        nbcode[Tvar[j]][2]=1;
-   dnewm=matrix(1,nlstate,1,npar);
+        nbcode[Tvar[j]][3]=2;
-   doldm=matrix(1,nlstate,1,nlstate);
+     */
+     ij=0; /* ij is similar to i but can jumps over null modalities */
-   hstepm=1*YEARM; /* Every year of age */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+         if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
-   agelim = AGESUP;
+           break;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+         }
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         ij++;
-     if (stepm >= YEARM) hstepm=1;
+         nbcode[Tvar[j]][ij]=i;  /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         cptcode = ij; /* New max modality for covar j */
-     gradg=matrix(1,npar,1,nlstate);
+     } /* end of loop on modality i=-1 to 1 or more */
-     gp=vector(1,nlstate);
-     gm=vector(1,nlstate);
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+     /*  /\*recode from 0 *\/ */
-     for(theta=1; theta <=npar; theta++){
+     /*                               k is a modality. If we have model=V1+V1*sex  */
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-       }
+     /*  } */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-       for(i=1;i<=nlstate;i++)
+     /*  if (ij > ncodemax[j]) { */
-         gp[i] = prlim[i][i];
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+     /*    break; */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     /*  } */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     /*   }  /\* end of loop on modality k *\/ */
-       for(i=1;i<=nlstate;i++)
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-         gm[i] = prlim[i][i];
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-       for(i=1;i<=nlstate;i++)
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-     } /* End theta */
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-     trgradg =matrix(1,nlstate,1,npar);
+    Ndum[ij]++; /* Might be supersed V1 + V1*age */
+  }
-     for(j=1; j<=nlstate;j++)
-       for(theta=1; theta <=npar; theta++)
+  ij=0;
-         trgradg[j][theta]=gradg[theta][j];
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     for(i=1;i<=nlstate;i++)
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-       varpl[i][(int)age] =0.;
+      ij++;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+      Tvaraff[ij]=i; /*For printing (unclear) */
-     for(i=1;i<=nlstate;i++)
+    }else{
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+        /* Tvaraff[ij]=0; */
+    }
-     fprintf(ficresvpl,"%.0f ",age );
+  }
-     for(i=1; i<=nlstate;i++)
+  /* ij--; */
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+  cptcoveff=ij; /*Number of total covariates*/
-     fprintf(ficresvpl,"\n");
-     free_vector(gp,1,nlstate);
+ }
-     free_vector(gm,1,nlstate);
-     free_matrix(gradg,1,npar,1,nlstate);
-     free_matrix(trgradg,1,nlstate,1,npar);
+ /*********** Health Expectancies ****************/
-   } /* End age */
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,npar);
+ {
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm;
- }
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
- /************ Variance of one-step probabilities  ******************/
+   double ***p3mat;
- 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 eip;
- {
-   int i, j=0,  i1, k1, l1, t, tj;
+   pstamp(ficreseij);
-   int k2, l2, j1,  z1;
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   int k=0,l, cptcode;
+   fprintf(ficreseij,"# Age");
-   int first=1, first1;
+   for(i=1; i<=nlstate;i++){
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+     for(j=1; j<=nlstate;j++){
-   double **dnewm,**doldm;
+       fprintf(ficreseij," e%1d%1d ",i,j);
-   double *xp;
+     }
-   double *gp, *gm;
+     fprintf(ficreseij," e%1d. ",i);
-   double **gradg, **trgradg;
+   }
-   double **mu;
+   fprintf(ficreseij,"\n");
-   double age,agelim, cov[NCOVMAX];
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+   if(estepm < stepm){
-   char fileresprob[FILENAMELENGTH];
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   char fileresprobcov[FILENAMELENGTH];
+   }
-   char fileresprobcor[FILENAMELENGTH];
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   double ***varpij;
+    * 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
-   strcpy(fileresprob,"prob");
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   strcat(fileresprob,fileres);
+    * progression in between and thus overestimating or underestimating according
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+    * to the curvature of the survival function. If, for the same date, we
-     printf("Problem with resultfile: %s\n", fileresprob);
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+    * to compare the new estimate of Life expectancy with the same linear
-   }
+    * hypothesis. A more precise result, taking into account a more precise
-   strcpy(fileresprobcov,"probcov");
+    * curvature will be obtained if estepm is as small as stepm. */
-   strcat(fileresprobcov,fileres);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+      nhstepm is the number of hstepm from age to agelim
-   }
+      nstepm is the number of stepm from age to agelin.
-   strcpy(fileresprobcor,"probcor");
+      Look at hpijx to understand the reason of that which relies in memory size
-   strcat(fileresprobcor,fileres);
+      and note for a fixed period like estepm months */
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+      survival function given by stepm (the optimization length). Unfortunately it
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+      means that if the survival funtion is printed only each two years of age and if
-   }
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+      results. So we changed our mind and took the option of the best precision.
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   */
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   agelim=AGESUP;
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   /* If stepm=6 months */
-   pstamp(ficresprob);
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-   fprintf(ficresprob,"# Age");
-   pstamp(ficresprobcov);
+ /* nhstepm age range expressed in number of stepm */
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   fprintf(ficresprobcov,"# Age");
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   pstamp(ficresprobcor);
+   /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   fprintf(ficresprobcor,"# Age");
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){
-   for(i=1; i<=nlstate;i++)
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     for(j=1; j<=(nlstate+ndeath);j++){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+     /* if (stepm >= YEARM) hstepm=1;*/
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+     /* If stepm=6 months */
-  /* fprintf(ficresprob,"\n");
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   fprintf(ficresprobcov,"\n");
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   fprintf(ficresprobcor,"\n");
-  */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-  xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     printf("%d|",(int)age);fflush(stdout);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+     /* Computing expectancies */
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     for(i=1; i<=nlstate;i++)
-   fprintf(fichtm,"\n");
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   file %s<br>\n",optionfilehtmcov);
+           /* 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(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
- and drawn. It helps understanding how is the covariance between two incidences.\
+         }
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   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. \
+     fprintf(ficreseij,"%3.0f",age );
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+     for(i=1; i<=nlstate;i++){
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+       eip=0;
- standard deviations wide on each axis. <br>\
+       for(j=1; j<=nlstate;j++){
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+         eip +=eij[i][j][(int)age];
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+       }
+       fprintf(ficreseij,"%9.4f", eip );
-   cov[1]=1;
+     }
-   tj=cptcoveff;
+     fprintf(ficreseij,"\n");
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   j1=0;
+   }
-   for(t=1; t<=tj;t++){
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(i1=1; i1<=ncodemax[t];i1++){
+   printf("\n");
-       j1++;
+   fprintf(ficlog,"\n");
-       if  (cptcovn>0) {
-         fprintf(ficresprob, "\n#********** Variable ");
+ }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresprob, "**********\n#\n");
+ 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(ficresprobcov, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ {
-         fprintf(ficresprobcov, "**********\n#\n");
+   /* Covariances of health expectancies eij and of total life expectancies according
+    to initial status i, ei. .
-         fprintf(ficgp, "\n#********** Variable ");
+   */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-         fprintf(ficgp, "**********\n#\n");
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
+   double ***p3matp, ***p3matm, ***varhe;
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+   double **dnewm,**doldm;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   double *xp, *xm;
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   int theta;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresprobcor, "**********\n#");
+   double eip, vip;
-       }
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-       for (age=bage; age<=fage; age ++){
+   xp=vector(1,npar);
-         cov[2]=age;
+   xm=vector(1,npar);
-         for (k=1; k<=cptcovn;k++) {
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-         }
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   pstamp(ficresstdeij);
-         for (k=1; k<=cptcovprod;k++)
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+     for(j=1; j<=nlstate;j++)
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+     fprintf(ficresstdeij," e%1d. ",i);
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   }
+   fprintf(ficresstdeij,"\n");
-         for(theta=1; theta <=npar; theta++){
-           for(i=1; i<=npar; i++)
+   pstamp(ficrescveij);
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
-           k=0;
+       cptj= (j-1)*nlstate+i;
-           for(i=1; i<= (nlstate); i++){
+       for(i2=1; i2<=nlstate;i2++)
-             for(j=1; j<=(nlstate+ndeath);j++){
+         for(j2=1; j2<=nlstate;j2++){
-               k=k+1;
+           cptj2= (j2-1)*nlstate+i2;
-               gp[k]=pmmij[i][j];
+           if(cptj2 <= cptj)
-             }
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-           }
+         }
+     }
-           for(i=1; i<=npar; i++)
+   fprintf(ficrescveij,"\n");
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   if(estepm < stepm){
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-           k=0;
+   }
-           for(i=1; i<=(nlstate); i++){
+   else  hstepm=estepm;
-             for(j=1; j<=(nlstate+ndeath);j++){
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-               k=k+1;
+    * This is mainly to measure the difference between two models: for example
-               gm[k]=pmmij[i][j];
+    * 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
-           }
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+    * to compare the new estimate of Life expectancy with the same linear
-         }
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-           for(theta=1; theta <=npar; theta++)
+   /* For example we decided to compute the life expectancy with the smallest unit */
-             trgradg[j][theta]=gradg[theta][j];
+   /* 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
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+      nstepm is the number of stepm from age to agelin.
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+      Look at hpijx to understand the reason of that which relies in memory size
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+      and note for a fixed period like estepm months */
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      survival function given by stepm (the optimization length). Unfortunately it
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+      results. So we changed our mind and took the option of the best precision.
+   */
-         k=0;
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
+   /* If stepm=6 months */
-             k=k+1;
+   /* nhstepm age range expressed in number of stepm */
-             mu[k][(int) age]=pmmij[i][j];
+   agelim=AGESUP;
-           }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-         }
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   /* if (stepm >= YEARM) hstepm=1;*/
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-             varpij[i][j][(int)age] = doldm[i][j];
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         /*printf("\n%d ",(int)age);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-           }*/
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-         fprintf(ficresprob,"\n%d ",(int)age);
+   for (age=bage; age<=fage; age ++){
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+     /* If stepm=6 months */
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-         }
-         i=0;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
+     /* Computing  Variances of health expectancies */
-             i=i++;
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+        decrease memory allocation */
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     for(theta=1; theta <=npar; theta++){
-             for (j=1; j<=i;j++){
+       for(i=1; i<=npar; i++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-             }
+       }
-           }
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-         }/* end of loop for state */
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       } /* end of loop for age */
+       for(j=1; j<= nlstate; j++){
-       /* Confidence intervalle of pij  */
+         for(i=1; i<=nlstate; i++){
-       /*
+           for(h=0; h<=nhstepm-1; h++){
-         fprintf(ficgp,"\nset noparametric;unset label");
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+           }
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+         }
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+       }
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       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];
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+         }
-       first1=1;
+     }/* End theta */
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
+     for(h=0; h<=nhstepm-1; h++)
-           j=(k2-1)*(nlstate+ndeath)+l2;
+       for(j=1; j<=nlstate*nlstate;j++)
-           for (k1=1; k1<=(nlstate);k1++){
+         for(theta=1; theta <=npar; theta++)
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+           trgradg[h][j][theta]=gradg[h][theta][j];
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
-               if(i<=j) continue;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-               for (age=bage; age<=fage; age ++){
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-                 if ((int)age %5==0){
+         varhe[ij][ji][(int)age] =0.;
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+      printf("%d|",(int)age);fflush(stdout);
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+      for(h=0;h<=nhstepm-1;h++){
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+       for(k=0;k<=nhstepm-1;k++){
-                   c12=cv12/sqrt(v1*v2);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-                   /* Computing eigen value of matrix of covariance */
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-                   /* Eigen vectors */
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+       }
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+     }
-                   v21=(lc1-v1)/cv12*v11;
-                   v12=-v21;
+     /* Computing expectancies */
-                   v22=v11;
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-                   tnalp=v21/v11;
+     for(i=1; i<=nlstate;i++)
-                   if(first1==1){
+       for(j=1; j<=nlstate;j++)
-                     first1=0;
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-                     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);
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-                   }
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-                   /*printf(fignu*/
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+         }
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-                   if(first==1){
+     fprintf(ficresstdeij,"%3.0f",age );
-                     first=0;
+     for(i=1; i<=nlstate;i++){
-                     fprintf(ficgp,"\nset parametric;unset label");
+       eip=0.;
-                     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);
+       vip=0.;
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+       for(j=1; j<=nlstate;j++){
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+         eip += eij[i][j][(int)age];
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+       }
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-                     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);
+     fprintf(ficresstdeij,"\n");
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+     fprintf(ficrescveij,"%3.0f",age );
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+     for(i=1; i<=nlstate;i++)
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       for(j=1; j<=nlstate;j++){
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+         cptj= (j-1)*nlstate+i;
-                   }else{
+         for(i2=1; i2<=nlstate;i2++)
-                     first=0;
+           for(j2=1; j2<=nlstate;j2++){
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+             cptj2= (j2-1)*nlstate+i2;
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+             if(cptj2 <= cptj)
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+           }
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       }
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+     fprintf(ficrescveij,"\n");
-                   }/* if first */
-                 } /* age mod 5 */
+   }
-               } /* end loop age */
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-               first=1;
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-             } /*l12 */
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-           } /* k12 */
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         } /*l1 */
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }/* k1 */
+   printf("\n");
-     } /* loop covariates */
+   fprintf(ficlog,"\n");
-   }
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   free_vector(xm,1,npar);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_vector(xp,1,npar);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_vector(xp,1,npar);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-   fclose(ficresprob);
+ }
-   fclose(ficresprobcov);
-   fclose(ficresprobcor);
+ /************ Variance ******************/
-   fflush(ficgp);
+ 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[])
-   fflush(fichtmcov);
+ {
- }
+   /* Variance of health expectancies */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /* double **newm;*/
- /******************* Printing html file ***********/
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-                   int lastpass, int stepm, int weightopt, char model[],\
+   int movingaverage();
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   double **dnewm,**doldm;
-                   int popforecast, int estepm ,\
+   double **dnewmp,**doldmp;
-                   double jprev1, double mprev1,double anprev1, \
+   int i, j, nhstepm, hstepm, h, nstepm ;
-                   double jprev2, double mprev2,double anprev2){
+   int k;
-   int jj1, k1, i1, cpt;
+   double *xp;
+   double **gp, **gm;  /* for var eij */
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   double ***gradg, ***trgradg; /*for var eij */
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   double **gradgp, **trgradgp; /* for var p point j */
- </ul>");
+   double *gpp, *gmp; /* for var p point j */
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+   double ***p3mat;
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   double age,agelim, hf;
-    fprintf(fichtm,"\
+   double ***mobaverage;
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   int theta;
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   char digit[4];
-    fprintf(fichtm,"\
+   char digitp[25];
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   char fileresprobmorprev[FILENAMELENGTH];
-    fprintf(fichtm,"\
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+   if(popbased==1){
-    <a href=\"%s\">%s</a> <br>\n",
+     if(mobilav!=0)
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+       strcpy(digitp,"-populbased-mobilav-");
-    fprintf(fichtm,"\
+     else strcpy(digitp,"-populbased-nomobil-");
-  - Population projections by age and states: \
+   }
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+   else
+     strcpy(digitp,"-stablbased-");
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+   if (mobilav!=0) {
-  m=cptcoveff;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-  jj1=0;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-  for(k1=1; k1<=m;k1++){
+     }
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   }
-      jj1++;
-      if (cptcovn > 0) {
+   strcpy(fileresprobmorprev,"prmorprev");
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   sprintf(digit,"%-d",ij);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-      }
+   strcat(fileresprobmorprev,fileres);
-      /* Pij */
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-      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> \
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-      /* Quasi-incidences */
+   }
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-  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> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-        /* Period (stable) prevalence in each health state */
+   pstamp(ficresprobmorprev);
-        for(cpt=1; cpt<nlstate;cpt++){
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-        }
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+     for(i=1; i<=nlstate;i++)
-         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> \
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+   }
-      }
+   fprintf(ficresprobmorprev,"\n");
-    } /* end i1 */
+   fprintf(ficgp,"\n# Routine varevsij");
-  }/* End k1 */
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-  fprintf(fichtm,"</ul>");
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ /*   } */
-  fprintf(fichtm,"\
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   pstamp(ficresvij);
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     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);
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+   else
-  fprintf(fichtm,"\
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   fprintf(ficresvij,"# Age");
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++)
-  fprintf(fichtm,"\
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   fprintf(ficresvij,"\n");
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-  fprintf(fichtm,"\
+   xp=vector(1,npar);
-  - 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): \
+   dnewm=matrix(1,nlstate,1,npar);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   doldm=matrix(1,nlstate,1,nlstate);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-  fprintf(fichtm,"\
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-  - (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>",
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   gpp=vector(nlstate+1,nlstate+ndeath);
-  fprintf(fichtm,"\
+   gmp=vector(nlstate+1,nlstate+ndeath);
-  - 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",
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-  fprintf(fichtm,"\
+   if(estepm < stepm){
-  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   }
-  fprintf(fichtm,"\
+   else  hstepm=estepm;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   /* For example we decided to compute the life expectancy with the smallest unit */
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   /* 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
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+      nstepm is the number of stepm from age to agelin.
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+      Look at function hpijx to understand why (it is linked to memory size questions) */
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- /*      <br>",fileres,fileres,fileres,fileres); */
+      survival function given by stepm (the optimization length). Unfortunately it
- /*  else  */
+      means that if the survival funtion is printed every two years of age and if
- /*    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); */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-  fflush(fichtm);
+      results. So we changed our mind and took the option of the best precision.
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-  m=cptcoveff;
+   agelim = AGESUP;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-  jj1=0;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-  for(k1=1; k1<=m;k1++){
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-      jj1++;
+     gp=matrix(0,nhstepm,1,nlstate);
-      if (cptcovn > 0) {
+     gm=matrix(0,nhstepm,1,nlstate);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     for(theta=1; theta <=npar; theta++){
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-      }
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+       }
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-      }
+       if (popbased==1) {
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+         if(mobilav ==0){
- health expectancies in states (1) and (2): %s%d.png<br>\
+           for(i=1; i<=nlstate;i++)
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+             prlim[i][i]=probs[(int)age][i][ij];
-    } /* end i1 */
+         }else{ /* mobilav */
-  }/* End k1 */
+           for(i=1; i<=nlstate;i++)
-  fprintf(fichtm,"</ul>");
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-  fflush(fichtm);
+         }
- }
+       }
- /******************* Gnuplot file **************/
+       for(j=1; j<= nlstate; j++){
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+         for(h=0; h<=nhstepm; h++){
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-   char dirfileres[132],optfileres[132];
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+         }
-   int ng;
+       }
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+       /* This for computing probability of death (h=1 means
- /*     printf("Problem with file %s",optionfilegnuplot); */
+          computed over hstepm matrices product = hstepm*stepm months)
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+          as a weighted average of prlim.
- /*   } */
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   /*#ifdef windows */
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-     /*#endif */
+       }
-   m=pow(2,cptcoveff);
+       /* end probability of death */
-   strcpy(dirfileres,optionfilefiname);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-   strcpy(optfileres,"vpl");
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-  /* 1eme*/
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-    for (k1=1; k1<= m ; k1 ++) {
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+       if (popbased==1) {
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+         if(mobilav ==0){
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+           for(i=1; i<=nlstate;i++)
- set ylabel \"Probability\" \n\
+             prlim[i][i]=probs[(int)age][i][ij];
- set ter png small\n\
+         }else{ /* mobilav */
- set size 0.65,0.65\n\
+           for(i=1; i<=nlstate;i++)
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-      for (i=1; i<= nlstate ; i ++) {
+       }
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-      }
+         for(h=0; h<=nhstepm; h++){
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-      for (i=1; i<= nlstate ; i ++) {
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         }
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-      }
+       /* This for computing probability of death (h=1 means
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+          computed over hstepm matrices product = hstepm*stepm months)
-      for (i=1; i<= nlstate ; i ++) {
+          as a weighted average of prlim.
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-      }
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-    }
+       }
-   }
+       /* end probability of death */
-   /*2 eme*/
+       for(j=1; j<= nlstate; j++) /* vareij */
-   for (k1=1; k1<= m ; k1 ++) {
+         for(h=0; h<=nhstepm; h++){
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+         }
-     for (i=1; i<= nlstate+1 ; i ++) {
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-       k=2*i;
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       }
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+     } /* End theta */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     for(h=0; h<=nhstepm; h++) /* veij */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for(j=1; j<=nlstate;j++)
-       for (j=1; j<= nlstate+1 ; j ++) {
+         for(theta=1; theta <=npar; theta++)
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           trgradg[h][j][theta]=gradg[h][theta][j];
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       fprintf(ficgp,"\" t\"\" w l 0,");
+       for(theta=1; theta <=npar; theta++)
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         trgradgp[j][theta]=gradgp[theta][j];
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       }
+     for(i=1;i<=nlstate;i++)
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       for(j=1;j<=nlstate;j++)
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+         vareij[i][j][(int)age] =0.;
-     }
-   }
+     for(h=0;h<=nhstepm;h++){
+       for(k=0;k<=nhstepm;k++){
-   /*3eme*/
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-   for (k1=1; k1<= m ; k1 ++) {
+         for(i=1;i<=nlstate;i++)
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+           for(j=1;j<=nlstate;j++)
-       /*       k=2+nlstate*(2*cpt-2); */
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-       k=2+(nlstate+1)*(cpt-1);
+       }
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+     }
-       fprintf(ficgp,"set ter png small\n\
- set size 0.65,0.65\n\
+     /* pptj */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         varppt[j][i]=doldmp[j][i];
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+     /* end ppptj */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+     /*  x centered again */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-       */
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-       for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+     if (popbased==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);*/
+       if(mobilav ==0){
+         for(i=1; i<=nlstate;i++)
-       }
+           prlim[i][i]=probs[(int)age][i][ij];
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+       }else{ /* mobilav */
-     }
+         for(i=1; i<=nlstate;i++)
-   }
+           prlim[i][i]=mobaverage[(int)age][i][ij];
+       }
-   /* CV preval stable (period) */
+     }
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+     /* This for computing probability of death (h=1 means
-       k=3;
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+        as a weighted average of prlim.
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+     */
- set ter png small\nset size 0.65,0.65\n\
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
- unset log y\n\
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
-       for (i=1; i< nlstate ; i ++)
+     /* end probability of death */
-         fprintf(ficgp,"+$%d",k+i+1);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       l=3+(nlstate+ndeath)*cpt;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+       for(i=1; i<=nlstate;i++){
-       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-         l=3+(nlstate+ndeath)*cpt;
+       }
-         fprintf(ficgp,"+$%d",l+i+1);
+     }
-       }
+     fprintf(ficresprobmorprev,"\n");
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-     }
+     fprintf(ficresvij,"%.0f ",age );
-   }
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-   /* proba elementaires */
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-   for(i=1,jk=1; i <=nlstate; i++){
+       }
-     for(k=1; k <=(nlstate+ndeath); k++){
+     fprintf(ficresvij,"\n");
-       if (k != i) {
+     free_matrix(gp,0,nhstepm,1,nlstate);
-         for(j=1; j <=ncovmodel; j++){
+     free_matrix(gm,0,nhstepm,1,nlstate);
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-           jk++;
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-           fprintf(ficgp,"\n");
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+   } /* End age */
-       }
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-     }
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-    }
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-      for(jk=1; jk <=m; jk++) {
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-        if (ng==2)
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-        else
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-        i=1;
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-        for(k2=1; k2<=nlstate; k2++) {
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-          k3=i;
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-          for(k=1; k<=(nlstate+ndeath); k++) {
+   /*  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);
-            if (k != k2){
+ */
-              if(ng==2)
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-              else
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+   free_vector(xp,1,npar);
-              ij=1;
+   free_matrix(doldm,1,nlstate,1,nlstate);
-              for(j=3; j <=ncovmodel; j++) {
+   free_matrix(dnewm,1,nlstate,1,npar);
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-                  ij++;
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                }
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                else
+   fclose(ficresprobmorprev);
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+   fflush(ficgp);
-              }
+   fflush(fichtm);
-              fprintf(ficgp,")/(1");
+ }  /* end varevsij */
-              for(k1=1; k1 <=nlstate; k1++){
+ /************ Variance of prevlim ******************/
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+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[])
-                ij=1;
+ {
-                for(j=3; j <=ncovmodel; j++){
+   /* Variance of prevalence limit */
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-                    ij++;
+   double **dnewm,**doldm;
-                  }
+   int i, j, nhstepm, hstepm;
-                  else
+   double *xp;
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+   double *gp, *gm;
-                }
+   double **gradg, **trgradg;
-                fprintf(ficgp,")");
+   double age,agelim;
-              }
+   int theta;
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+   pstamp(ficresvpl);
-              i=i+ncovmodel;
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-            }
+   fprintf(ficresvpl,"# Age");
-          } /* end k */
+   for(i=1; i<=nlstate;i++)
-        } /* end k2 */
+       fprintf(ficresvpl," %1d-%1d",i,i);
-      } /* end jk */
+   fprintf(ficresvpl,"\n");
-    } /* end ng */
-    fflush(ficgp);
+   xp=vector(1,npar);
- }  /* end gnuplot */
+   dnewm=matrix(1,nlstate,1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
- /*************** Moving average **************/
+   hstepm=1*YEARM; /* Every year of age */
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGESUP;
-   int i, cpt, cptcod;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   int modcovmax =1;
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   int mobilavrange, mob;
+     if (stepm >= YEARM) hstepm=1;
-   double age;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     gradg=matrix(1,npar,1,nlstate);
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+     gp=vector(1,nlstate);
-                            a covariate has 2 modalities */
+     gm=vector(1,nlstate);
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+     for(theta=1; theta <=npar; theta++){
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-     if(mobilav==1) mobilavrange=5; /* default */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     else mobilavrange=mobilav;
+       }
-     for (age=bage; age<=fage; age++)
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       for (i=1; i<=nlstate;i++)
+       for(i=1;i<=nlstate;i++)
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+         gp[i] = prlim[i][i];
-           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<=npar; i++) /* Computes gradient */
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-        we use a 5 terms etc. until the borders are no more concerned.
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-     */
+       for(i=1;i<=nlstate;i++)
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+         gm[i] = prlim[i][i];
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-         for (i=1; i<=nlstate;i++){
+       for(i=1;i<=nlstate;i++)
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+     } /* End theta */
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+     trgradg =matrix(1,nlstate,1,npar);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               }
+     for(j=1; j<=nlstate;j++)
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+       for(theta=1; theta <=npar; theta++)
-           }
+         trgradg[j][theta]=gradg[theta][j];
-         }
-       }/* end age */
+     for(i=1;i<=nlstate;i++)
-     }/* end mob */
+       varpl[i][(int)age] =0.;
-   }else return -1;
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-   return 0;
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
- }/* End movingaverage */
+     for(i=1;i<=nlstate;i++)
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
- /************** Forecasting ******************/
+     fprintf(ficresvpl,"%.0f ",age );
- 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){
+     for(i=1; i<=nlstate;i++)
-   /* proj1, year, month, day of starting projection
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-      agemin, agemax range of age
+     fprintf(ficresvpl,"\n");
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+     free_vector(gp,1,nlstate);
-      anproj2 year of en of projection (same day and month as proj1).
+     free_vector(gm,1,nlstate);
-   */
+     free_matrix(gradg,1,npar,1,nlstate);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+     free_matrix(trgradg,1,nlstate,1,npar);
-   int *popage;
+   } /* End age */
-   double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   free_vector(xp,1,npar);
-   double *popeffectif,*popcount;
+   free_matrix(doldm,1,nlstate,1,npar);
-   double ***p3mat;
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   double ***mobaverage;
-   char fileresf[FILENAMELENGTH];
+ }
-   agelim=AGESUP;
+ /************ Variance of one-step probabilities  ******************/
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ 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[])
+ {
-   strcpy(fileresf,"f");
+   int i, j=0,  k1, l1, tj;
-   strcat(fileresf,fileres);
+   int k2, l2, j1,  z1;
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+   int k=0, l;
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+   int first=1, first1, first2;
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   }
+   double **dnewm,**doldm;
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   double *xp;
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   double *gp, *gm;
+   double **gradg, **trgradg;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   double **mu;
+   double age, cov[NCOVMAX+1];
-   if (mobilav!=0) {
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   int theta;
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   char fileresprob[FILENAMELENGTH];
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   char fileresprobcov[FILENAMELENGTH];
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   char fileresprobcor[FILENAMELENGTH];
-     }
+   double ***varpij;
-   }
+   strcpy(fileresprob,"prob");
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   strcat(fileresprob,fileres);
-   if (stepm<=12) stepsize=1;
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-   if(estepm < stepm){
+     printf("Problem with resultfile: %s\n", fileresprob);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    }
-   else  hstepm=estepm;
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
-   hstepm=hstepm/stepm;
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-                                fractional in yp1 */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   anprojmean=yp;
+   }
-   yp2=modf((yp1*12),&yp);
+   strcpy(fileresprobcor,"probcor");
-   mprojmean=yp;
+   strcat(fileresprobcor,fileres);
-   yp1=modf((yp2*30.5),&yp);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-   jprojmean=yp;
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-   if(jprojmean==0) jprojmean=1;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   if(mprojmean==0) jprojmean=1;
+   }
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   i1=cptcoveff;
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   if (cptcovn < 1){i1=1;}
+   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(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   pstamp(ficresprob);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- /*            if (h==(int)(YEARM*yearp)){ */
+   fprintf(ficresprob,"# Age");
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   pstamp(ficresprobcov);
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-       k=k+1;
+   fprintf(ficresprobcov,"# Age");
-       fprintf(ficresf,"\n#******");
+   pstamp(ficresprobcor);
-       for(j=1;j<=cptcoveff;j++) {
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   fprintf(ficresprobcor,"# Age");
-       }
-       fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+   for(i=1; i<=nlstate;i++)
-       for(j=1; j<=nlstate+ndeath;j++){
+     for(j=1; j<=(nlstate+ndeath);j++){
-         for(i=1; i<=nlstate;i++)
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-           fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-         fprintf(ficresf," p.%d",j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-       }
+     }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+  /* fprintf(ficresprob,"\n");
-         fprintf(ficresf,"\n");
+   fprintf(ficresprobcov,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   fprintf(ficresprobcor,"\n");
+  */
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+   xp=vector(1,npar);
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-           nhstepm = nhstepm/hstepm;
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-           oldm=oldms;savm=savms;
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+   first=1;
+   fprintf(ficgp,"\n# Routine varprob");
-           for (h=0; h<=nhstepm; h++){
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-             if (h*hstepm/YEARM*stepm ==yearp) {
+   fprintf(fichtm,"\n");
-               fprintf(ficresf,"\n");
-               for(j=1;j<=cptcoveff;j++)
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+   file %s<br>\n",optionfilehtmcov);
-             }
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-             for(j=1; j<=nlstate+ndeath;j++) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-               ppij=0.;
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-               for(i=1; i<=nlstate;i++) {
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-                 if (mobilav==1)
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-                 else {
+ standard deviations wide on each axis. <br>\
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+  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>\
-                 if (h*hstepm/YEARM*stepm== yearp) {
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
+   cov[1]=1;
-               } /* end i */
+   /* tj=cptcoveff; */
-               if (h*hstepm/YEARM*stepm==yearp) {
+   tj = (int) pow(2,cptcoveff);
-                 fprintf(ficresf," %.3f", ppij);
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-               }
+   j1=0;
-             }/* end j */
+   for(j1=1; j1<=tj;j1++){
-           } /* end h */
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /*j1++;*/
-         } /* end agec */
+       if  (cptcovn>0) {
-       } /* end yearp */
+         fprintf(ficresprob, "\n#********** Variable ");
-     } /* end cptcod */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   } /* end  cptcov */
+         fprintf(ficresprob, "**********\n#\n");
+         fprintf(ficresprobcov, "\n#********** Variable ");
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#\n");
-   fclose(ficresf);
- }
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- /************** Forecasting *****not tested NB*************/
+         fprintf(ficgp, "**********\n#\n");
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-   int *popage;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   double calagedatem, agelim, kk1, kk2;
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-   double *popeffectif,*popcount;
-   double ***p3mat,***tabpop,***tabpopprev;
+         fprintf(ficresprobcor, "\n#********** Variable ");
-   double ***mobaverage;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   char filerespop[FILENAMELENGTH];
+         fprintf(ficresprobcor, "**********\n#");
+       }
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-   agelim=AGESUP;
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
+         if(nagesqr==1)
-   strcpy(filerespop,"pop");
+           cov[3]= age*age;
-   strcat(filerespop,fileres);
+         for (k=1; k<=cptcovn;k++) {
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+                                                          * 1  1 1 1 1
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+                                                          * 2  2 1 1 1
-   }
+                                                          * 3  1 2 1 1
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+                                                          */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+         }
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
-   if (mobilav!=0) {
+         for (k=1; k<=cptcovprod;k++)
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         for(theta=1; theta <=npar; theta++){
-     }
+           for(i=1; i<=npar; i++)
-   }
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   if (stepm<=12) stepsize=1;
+           k=0;
-   agelim=AGESUP;
+           for(i=1; i<= (nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
-   hstepm=1;
+               k=k+1;
-   hstepm=hstepm/stepm;
+               gp[k]=pmmij[i][j];
+             }
-   if (popforecast==1) {
+           }
-     if((ficpop=fopen(popfile,"r"))==NULL) {
-       printf("Problem with population file : %s\n",popfile);exit(0);
+           for(i=1; i<=npar; i++)
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-     }
-     popage=ivector(0,AGESUP);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     popeffectif=vector(0,AGESUP);
+           k=0;
-     popcount=vector(0,AGESUP);
+           for(i=1; i<=(nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
-     i=1;
+               k=k+1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+               gm[k]=pmmij[i][j];
+             }
-     imx=i;
+           }
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+         }
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       k=k+1;
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-       fprintf(ficrespop,"\n#******");
+           for(theta=1; theta <=npar; theta++)
-       for(j=1;j<=cptcoveff;j++) {
+             trgradg[j][theta]=gradg[theta][j];
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       fprintf(ficrespop,"******\n");
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-       fprintf(ficrespop,"# Age");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+         k=0;
-       for (cpt=0; cpt<=0;cpt++) {
+         for(i=1; i<=(nlstate); i++){
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+           for(j=1; j<=(nlstate+ndeath);j++){
+             k=k+1;
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+             mu[k][(int) age]=pmmij[i][j];
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           }
-           nhstepm = nhstepm/hstepm;
+         }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-           oldm=oldms;savm=savms;
+             varpij[i][j][(int)age] = doldm[i][j];
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         /*printf("\n%d ",(int)age);
-           for (h=0; h<=nhstepm; h++){
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-             }
+           }*/
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
+         fprintf(ficresprob,"\n%d ",(int)age);
-               for(i=1; i<=nlstate;i++) {
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-                 if (mobilav==1)
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-                 }
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-               }
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-               if (h==(int)(calagedatem+12*cpt)){
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+         }
-                   /*fprintf(ficrespop," %.3f", kk1);
+         i=0;
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+         for (k=1; k<=(nlstate);k++){
-               }
+           for (l=1; l<=(nlstate+ndeath);l++){
-             }
+             i++;
-             for(i=1; i<=nlstate;i++){
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-               kk1=0.;
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-                 for(j=1; j<=nlstate;j++){
+             for (j=1; j<=i;j++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-                 }
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              }
+           }
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+         }/* end of loop for state */
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+       } /* end of loop for age */
-           }
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         }
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       }
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   /******/
+       /* Confidence intervalle of pij  */
+       /*
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficgp,"\nunset parametric;unset label");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+         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);
-           nhstepm = nhstepm/hstepm;
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-           oldm=oldms;savm=savms;
+       */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           for (h=0; h<=nhstepm; h++){
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       first1=1;first2=2;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       for (k2=1; k2<=(nlstate);k2++){
-             }
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-             for(j=1; j<=nlstate+ndeath;j++) {
+           if(l2==k2) continue;
-               kk1=0.;kk2=0;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-               for(i=1; i<=nlstate;i++) {
+           for (k1=1; k1<=(nlstate);k1++){
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               }
+               if(l1==k1) continue;
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+               i=(k1-1)*(nlstate+ndeath)+l1;
-             }
+               if(i<=j) continue;
-           }
+               for (age=bage; age<=fage; age ++){
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                 if ((int)age %5==0){
-         }
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-       }
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-    }
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-   }
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
-   if (popforecast==1) {
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     free_ivector(popage,0,AGESUP);
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     free_vector(popeffectif,0,AGESUP);
+                   if ((lc2 <0) || (lc1 <0) ){
-     free_vector(popcount,0,AGESUP);
+                     if(first2==1){
-   }
+                       first1=0;
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                     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);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                     }
-   fclose(ficrespop);
+                     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);
- } /* End of popforecast */
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                     /* lc2=fabs(lc2); */
- int fileappend(FILE *fichier, char *optionfich)
+                   }
- {
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+                   /* Eigen vectors */
-     printf("Problem with file: %s\n", optionfich);
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-     return (0);
+                   v21=(lc1-v1)/cv12*v11;
-   }
+                   v12=-v21;
-   fflush(fichier);
+                   v22=v11;
-   return (1);
+                   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);
- /**************** function prwizard **********************/
+                   }
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
- {
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-   /* Wizard to print covariance matrix template */
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                   if(first==1){
-   char ca[32], cb[32], cc[32];
+                     first=0;
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+                     fprintf(ficgp,"\nset parametric;unset label");
-   int numlinepar;
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-   for(i=1; i <=nlstate; i++){
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-     jj=0;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-     for(j=1; j <=nlstate+ndeath; j++){
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       if(j==i) continue;
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       jj++;
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       printf("%1d%1d",i,j);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-       fprintf(ficparo,"%1d%1d",i,j);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-       for(k=1; k<=ncovmodel;k++){
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-         /*        printf(" %lf",param[i][j][k]); */
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-         printf(" 0.");
+                   }else{
-         fprintf(ficparo," 0.");
+                     first=0;
-       }
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-       printf("\n");
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-       fprintf(ficparo,"\n");
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-     }
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-   }
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   printf("# Scales (for hessian or gradient estimation)\n");
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+                   }/* if first */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                 } /* age mod 5 */
-   for(i=1; i <=nlstate; i++){
+               } /* end loop age */
-     jj=0;
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-     for(j=1; j <=nlstate+ndeath; j++){
+               first=1;
-       if(j==i) continue;
+             } /*l12 */
-       jj++;
+           } /* k12 */
-       fprintf(ficparo,"%1d%1d",i,j);
+         } /*l1 */
-       printf("%1d%1d",i,j);
+       }/* k1 */
-       fflush(stdout);
+       /* } */ /* loop covariates */
-       for(k=1; k<=ncovmodel;k++){
+   }
-         /*      printf(" %le",delti3[i][j][k]); */
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-         printf(" 0.");
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-         fprintf(ficparo," 0.");
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-       }
+   free_vector(xp,1,npar);
-       numlinepar++;
+   fclose(ficresprob);
-       printf("\n");
+   fclose(ficresprobcov);
-       fprintf(ficparo,"\n");
+   fclose(ficresprobcor);
-     }
+   fflush(ficgp);
-   }
+   fflush(fichtmcov);
-   printf("# Covariance matrix\n");
+ }
- /* # 121 Var(a12)\n\ */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /******************* Printing html file ***********/
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                   int lastpass, int stepm, int weightopt, char model[],\
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+                   int popforecast, int estepm ,\
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+                   double jprev1, double mprev1,double anprev1, \
-   fflush(stdout);
+                   double jprev2, double mprev2,double anprev2){
-   fprintf(ficparo,"# Covariance matrix\n");
+   int jj1, k1, i1, cpt;
-   /* # 121 Var(a12)\n\ */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   /* #   ...\n\ */
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+ </ul>");
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-   for(itimes=1;itimes<=2;itimes++){
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-     jj=0;
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-     for(i=1; i <=nlstate; i++){
+    fprintf(fichtm,"\
-       for(j=1; j <=nlstate+ndeath; j++){
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-         if(j==i) continue;
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-         for(k=1; k<=ncovmodel;k++){
+    fprintf(fichtm,"\
-           jj++;
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-           ca[0]= k+'a'-1;ca[1]='\0';
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-           if(itimes==1){
+    fprintf(fichtm,"\
-             printf("#%1d%1d%d",i,j,k);
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+    <a href=\"%s\">%s</a> <br>\n",
-           }else{
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-             printf("%1d%1d%d",i,j,k);
+    fprintf(fichtm,"\
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+  - Population projections by age and states: \
-             /*  printf(" %.5le",matcov[i][j]); */
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-           }
-           ll=0;
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-           for(li=1;li <=nlstate; li++){
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+  m=pow(2,cptcoveff);
-               if(lj==li) continue;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-               for(lk=1;lk<=ncovmodel;lk++){
-                 ll++;
+  jj1=0;
-                 if(ll<=jj){
+  for(k1=1; k1<=m;k1++){
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-                   if(ll<jj){
+      jj1++;
-                     if(itimes==1){
+      if (cptcovn > 0) {
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-                     }else{
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-                       printf(" 0.");
+          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
-                       fprintf(ficparo," 0.");
+        }
-                     }
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-                   }else{
+      }
-                     if(itimes==1){
+      /* Pij */
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                     }else{
+      /* Quasi-incidences */
-                       printf(" 0.");
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-                       fprintf(ficparo," 0.");
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-                     }
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                   }
+        /* Period (stable) prevalence in each health state */
-                 }
+        for(cpt=1; cpt<=nlstate;cpt++){
-               } /* end lk */
+          fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
-             } /* end lj */
+ <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-           } /* end li */
+        }
-           printf("\n");
+      for(cpt=1; cpt<=nlstate;cpt++) {
-           fprintf(ficparo,"\n");
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-           numlinepar++;
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-         } /* end k*/
+      }
-       } /*end j */
+    /* } /\* end i1 *\/ */
-     } /* end i */
+  }/* End k1 */
-   } /* end itimes */
+  fprintf(fichtm,"</ul>");
- } /* end of prwizard */
+  fprintf(fichtm,"\
- /******************* Gompertz Likelihood ******************************/
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- double gompertz(double x[])
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
- {
+  - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
-   double A,B,L=0.0,sump=0.,num=0.;
-   int i,n=0; /* n is the size of the sample */
+  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-   for (i=0;i<=imx-1 ; i++) {
+  fprintf(fichtm,"\
-     sump=sump+weight[i];
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     /*    sump=sump+1;*/
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-     num=num+1;
-   }
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-   /* for (i=0; i<=imx; i++)
+  fprintf(fichtm,"\
-      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]);*/
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   for (i=1;i<=imx ; i++)
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-     {
+  fprintf(fichtm,"\
-       if (cens[i] == 1 && wav[i]>1)
+  - (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=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-       if (cens[i] == 0 && wav[i]>1)
+  fprintf(fichtm,"\
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+  - 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",
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+  - 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",
-       if (wav[i] > 1 ) { /* ??? */
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-         L=L+A*weight[i];
+  fprintf(fichtm,"\
-         /*      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]);*/
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-       }
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-     }
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ /*  - 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 */
-   return -2*L*num/sump;
+ /*      <br>",fileres,fileres,fileres,fileres); */
- }
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- /******************* Printing html file ***********/
+  fflush(fichtm);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,  double p[],double **matcov,double agemortsup){
+  m=pow(2,cptcoveff);
-   int i,k;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+  jj1=0;
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+  for(k1=1; k1<=m;k1++){
-   for (i=1;i<=2;i++)
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-     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]));
+      jj1++;
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+      if (cptcovn > 0) {
-   fprintf(fichtm,"</ul>");
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
-  for (k=agegomp;k<(agemortsup-2);k++)
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-    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]);
+ 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);
+      }
-   fflush(fichtm);
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- }
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
- /******************* Gnuplot file **************/
+  drawn in addition to the population based expectancies computed using\
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   char dirfileres[132],optfileres[132];
+    /* } /\* end i1 *\/ */
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  }/* End k1 */
-   int ng;
+  fprintf(fichtm,"</ul>");
+  fflush(fichtm);
+ }
-   /*#ifdef windows */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+ /******************* Gnuplot file **************/
-     /*#endif */
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
-   strcpy(dirfileres,optionfilefiname);
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   strcpy(optfileres,"vpl");
+   int ng=0;
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   fprintf(ficgp, "set ter png small\n set log y\n");
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-   fprintf(ficgp, "set size 0.65,0.65\n");
+ /*   } */
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+   /*#ifdef windows */
- }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   m=pow(2,cptcoveff);
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
- /***********************************************/
+  /* 1eme*/
- /**************** Main Program *****************/
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
- /***********************************************/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
- int main(int argc, char *argv[])
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
- {
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+ set ylabel \"Probability\" \n\
-   int linei, month, year,iout;
+ set ter png small size 320, 240\n\
-   int jj, ll, li, lj, lk, imk;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-   int numlinepar=0; /* Current linenumber of parameter file */
-   int itimes;
+      for (i=1; i<= nlstate ; i ++) {
-   int NDIM=2;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-   char ca[32], cb[32], cc[32];
+      }
-   char dummy[]="                         ";
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-   /*  FILE *fichtm; *//* Html File */
+      for (i=1; i<= nlstate ; i ++) {
-   /* FILE *ficgp;*/ /*Gnuplot File */
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-   struct stat info;
+        else fprintf(ficgp," %%*lf (%%*lf)");
-   double agedeb, agefin,hf;
+      }
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
-   double fret;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-   double **xi,tmp,delta;
+        else fprintf(ficgp," %%*lf (%%*lf)");
+      }
-   double dum; /* Dummy variable */
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-   double ***p3mat;
+    }
-   double ***mobaverage;
+   }
-   int *indx;
+   /*2 eme*/
-   char line[MAXLINE], linepar[MAXLINE];
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   for (k1=1; k1<= m ; k1 ++) {
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-   char **bp, *tok, *val; /* pathtot */
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+     for (i=1; i<= nlstate+1 ; i ++) {
-   int c,  h , cpt,l;
+       k=2*i;
-   int ju,jl, mi;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+       for (j=1; j<= nlstate+1 ; j ++) {
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+         else fprintf(ficgp," %%*lf (%%*lf)");
-   int mobilav=0,popforecast=0;
+       }
-   int hstepm, nhstepm;
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-   int agemortsup;
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-   float  sumlpop=0.;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+       for (j=1; j<= nlstate+1 ; j ++) {
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
+         else fprintf(ficgp," %%*lf (%%*lf)");
-   double bage, fage, age, agelim, agebase;
+       }
-   double ftolpl=FTOL;
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-   double **prlim;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   double *severity;
+       for (j=1; j<= nlstate+1 ; j ++) {
-   double ***param; /* Matrix of parameters */
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-   double  *p;
+         else fprintf(ficgp," %%*lf (%%*lf)");
-   double **matcov; /* Matrix of covariance */
+       }
-   double ***delti3; /* Scale */
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-   double *delti; /* Scale */
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-   double ***eij, ***vareij;
+     }
-   double **varpl; /* Variances of prevalence limits by age */
+   }
-   double *epj, vepp;
-   double kk1, kk2;
+   /*3eme*/
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   double **ximort;
+   for (k1=1; k1<= m ; k1 ++) {
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-   int *dcwave;
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
-   char z[1]="c", occ;
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-   char  *strt, strtend[80];
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-   char *stratrunc;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-   int lstra;
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-   long total_usecs;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- /*   setlocale (LC_ALL, ""); */
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       */
- /*   textdomain (PACKAGE); */
+       for (i=1; i< nlstate ; i ++) {
- /*   setlocale (LC_CTYPE, ""); */
+         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);
- /*   setlocale (LC_MESSAGES, ""); */
+         /*      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);*/
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       }
-   (void) gettimeofday(&start_time,&tzp);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-   curr_time=start_time;
+     }
-   tm = *localtime(&start_time.tv_sec);
+   }
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+   /* CV preval stable (period) */
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
- /*  printf("Localtime (at start)=%s",strstart); */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+       k=3;
- /*  tm = *localtime(&start_time.tv_sec); */
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ set ter png small size 320, 240\n\
- /*   tp.tv_sec = mktime(&tmg); */
+ unset log y\n\
- /*   strt=asctime(&tmg); */
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
- /*   printf("Time(after) =%s",strstart);  */
+       for (i=1; i<= nlstate ; i ++){
- /*  (void) time (&time_value);
+         if(i==1)
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
- *  tm = *localtime(&time_value);
+         else
- *  strstart=asctime(&tm);
+           fprintf(ficgp,", '' ");
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+         l=(nlstate+ndeath)*(i-1)+1;
- */
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=1; j<= (nlstate-1) ; j ++)
-   nberr=0; /* Number of errors and warnings */
+           fprintf(ficgp,"+$%d",k+l+j);
-   nbwarn=0;
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-   getcwd(pathcd, size);
+       } /* nlstate */
+       fprintf(ficgp,"\n");
-   printf("\n%s\n%s",version,fullversion);
+     } /* end cpt state*/
-   if(argc <=1){
+   } /* end covariate */
-     printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+   /* proba elementaires */
-     i=strlen(pathr);
+   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
-     if(pathr[i-1]=='\n')
+   for(i=1,jk=1; i <=nlstate; i++){
-       pathr[i-1]='\0';
+     fprintf(ficgp,"# initial state %d\n",i);
-    for (tok = pathr; tok != NULL; ){
+     for(k=1; k <=(nlstate+ndeath); k++){
-       printf("Pathr |%s|\n",pathr);
+       if (k != i) {
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+         fprintf(ficgp,"#   current state %d\n",k);
-       printf("val= |%s| pathr=%s\n",val,pathr);
+         for(j=1; j <=ncovmodel; j++){
-       strcpy (pathtot, val);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-       if(pathr[0] == '\0') break; /* Dirty */
+           jk++;
-     }
+         }
-   }
+         fprintf(ficgp,"\n");
-   else{
+       }
-     strcpy(pathtot,argv[1]);
+     }
-   }
+    }
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   fprintf(ficgp,"##############\n#\n");
-   /*cygwin_split_path(pathtot,path,optionfile);
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /*goto avoid;*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
+   fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
-   /* Split argv[0], imach program to get pathimach */
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-  /*   strcpy(pathimach,argv[0]); */
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
-   chdir(path); /* Can be a relative path */
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
-     printf("Current directory %s!\n",pathcd);
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
-   strcpy(command,"mkdir ");
+   fprintf(ficgp,"#\n");
-   strcat(command,optionfilefiname);
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   if((outcmd=system(command)) != 0){
+      fprintf(ficgp,"# ng=%d\n",ng);
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+      for(jk=1; jk <=m; jk++) {
-     /* fclose(ficlog); */
+        fprintf(ficgp,"#    jk=%d\n",jk);
- /*     exit(1); */
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-   }
+        if (ng==2)
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
- /*     perror("mkdir"); */
+        else
- /*   } */
+          fprintf(ficgp,"\nset title \"Probability\"\n");
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   /*-------- arguments in the command line --------*/
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
-   /* Log file */
+          k3=i;
-   strcat(filelog, optionfilefiname);
+          for(k=1; k<=(nlstate+ndeath); k++) {
-   strcat(filelog,".log");    /* */
+            if (k != k2){
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+              if(ng==2)
-     printf("Problem with logfile %s\n",filelog);
+                if(nagesqr==0)
-     goto end;
+                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-   }
+                else /* nagesqr =1 */
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+              else
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+                if(nagesqr==0)
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-  path=%s \n\
+                else /* nagesqr =1 */
-  optionfile=%s\n\
+                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-  optionfilext=%s\n\
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+              for(j=3; j <=ncovmodel-nagesqr; j++) {
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
-   printf("Local time (at start):%s",strstart);
+                  fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+                  ij++;
-   fflush(ficlog);
+                }
- /*   (void) gettimeofday(&curr_time,&tzp); */
+                else
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+              }
-   /* */
+              fprintf(ficgp,")/(1");
-   strcpy(fileres,"r");
-   strcat(fileres, optionfilefiname);
+              for(k1=1; k1 <=nlstate; k1++){
-   strcat(fileres,".txt");    /* Other files have txt extension */
+                if(nagesqr==0)
+                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-   /*---------arguments file --------*/
+                else /* nagesqr =1 */
+                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
+                ij=1;
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+                for(j=3; j <=ncovmodel-nagesqr; j++){
-     fflush(ficlog);
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-     goto end;
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-   }
+                    ij++;
+                  }
+                  else
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   strcpy(filereso,"o");
+                }
-   strcat(filereso,fileres);
+                fprintf(ficgp,")");
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+              }
-     printf("Problem with Output resultfile: %s\n", filereso);
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-     fflush(ficlog);
+              i=i+ncovmodel;
-     goto end;
+            }
-   }
+          } /* end k */
+        } /* end k2 */
-   /* Reads comments: lines beginning with '#' */
+      } /* end jk */
-   numlinepar=0;
+    } /* end ng */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+  /* avoid: */
-     ungetc(c,ficpar);
+    fflush(ficgp);
-     fgets(line, MAXLINE, ficpar);
+ }  /* end gnuplot */
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
+ /*************** Moving average **************/
-     fputs(line,ficlog);
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-   }
-   ungetc(c,ficpar);
+   int i, cpt, cptcod;
+   int modcovmax =1;
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   int mobilavrange, mob;
-   numlinepar++;
+   double age;
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-   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);
+                            a covariate has 2 modalities */
-   fflush(ficlog);
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-     fgets(line, MAXLINE, ficpar);
+     if(mobilav==1) mobilavrange=5; /* default */
-     numlinepar++;
+     else mobilavrange=mobilav;
-     puts(line);
+     for (age=bage; age<=fage; age++)
-     fputs(line,ficparo);
+       for (i=1; i<=nlstate;i++)
-     fputs(line,ficlog);
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-   }
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   ungetc(c,ficpar);
+     /* We keep the original values on the extreme ages bage, fage and for
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+        we use a 5 terms etc. until the borders are no more concerned.
-   covar=matrix(0,NCOVMAX,1,n);
+     */
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+         for (i=1; i<=nlstate;i++){
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-   delti=delti3[1][1];
+               }
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+           }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+         }
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       }/* end age */
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     }/* end mob */
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   }else return -1;
-     fclose (ficparo);
+   return 0;
-     fclose (ficlog);
+ }/* End movingaverage */
-     goto end;
-     exit(0);
-   }
+ /************** Forecasting ******************/
-   else if(mle==-3) {
+ 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){
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+   /* proj1, year, month, day of starting projection
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+      agemin, agemax range of age
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+      anproj2 year of en of projection (same day and month as proj1).
-     matcov=matrix(1,npar,1,npar);
+   */
-   }
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
-   else{
+   double agec; /* generic age */
-     /* Read guess parameters */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-     /* Reads comments: lines beginning with '#' */
+   double *popeffectif,*popcount;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   double ***p3mat;
-       ungetc(c,ficpar);
+   double ***mobaverage;
-       fgets(line, MAXLINE, ficpar);
+   char fileresf[FILENAMELENGTH];
-       numlinepar++;
-       puts(line);
+   agelim=AGESUP;
-       fputs(line,ficparo);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-       fputs(line,ficlog);
-     }
+   strcpy(fileresf,"f");
-     ungetc(c,ficpar);
+   strcat(fileresf,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-     for(i=1; i <=nlstate; i++){
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-       j=0;
+   }
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-         if(jj==i) continue;
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-         j++;
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-         if ((i1 != i) && (j1 != j)){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+   if (mobilav!=0) {
- It might be a problem of design; if ncovcol and the model are correct\n \
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-           exit(1);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         }
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+     }
-         if(mle==1)
+   }
-           printf("%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-         for(k=1; k<=ncovmodel;k++){
+   if (stepm<=12) stepsize=1;
-           fscanf(ficpar," %lf",&param[i][j][k]);
+   if(estepm < stepm){
-           if(mle==1){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-             printf(" %lf",param[i][j][k]);
+   }
-             fprintf(ficlog," %lf",param[i][j][k]);
+   else  hstepm=estepm;
-           }
-           else
+   hstepm=hstepm/stepm;
-             fprintf(ficlog," %lf",param[i][j][k]);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-           fprintf(ficparo," %lf",param[i][j][k]);
+                                fractional in yp1 */
-         }
+   anprojmean=yp;
-         fscanf(ficpar,"\n");
+   yp2=modf((yp1*12),&yp);
-         numlinepar++;
+   mprojmean=yp;
-         if(mle==1)
+   yp1=modf((yp2*30.5),&yp);
-           printf("\n");
+   jprojmean=yp;
-         fprintf(ficlog,"\n");
+   if(jprojmean==0) jprojmean=1;
-         fprintf(ficparo,"\n");
+   if(mprojmean==0) jprojmean=1;
-       }
-     }
+   i1=cptcoveff;
-     fflush(ficlog);
+   if (cptcovn < 1){i1=1;}
-     p=param[1][1];
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-     /* Reads comments: lines beginning with '#' */
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+ /*            if (h==(int)(YEARM*yearp)){ */
-       fgets(line, MAXLINE, ficpar);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-       numlinepar++;
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       puts(line);
+       k=k+1;
-       fputs(line,ficparo);
+       fprintf(ficresf,"\n#******");
-       fputs(line,ficlog);
+       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]]);
-     ungetc(c,ficpar);
+       }
+       fprintf(ficresf,"******\n");
-     for(i=1; i <=nlstate; i++){
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       for(j=1; j<=nlstate+ndeath;j++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         for(i=1; i<=nlstate;i++)
-         if ((i1-i)*(j1-j)!=0){
+           fprintf(ficresf," p%d%d",i,j);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         fprintf(ficresf," p.%d",j);
-           exit(1);
+       }
-         }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-         printf("%1d%1d",i,j);
+         fprintf(ficresf,"\n");
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-         fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-           printf(" %le",delti3[i][j][k]);
+           nhstepm = nhstepm/hstepm;
-           fprintf(ficparo," %le",delti3[i][j][k]);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficlog," %le",delti3[i][j][k]);
+           oldm=oldms;savm=savms;
-         }
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-         fscanf(ficpar,"\n");
-         numlinepar++;
+           for (h=0; h<=nhstepm; h++){
-         printf("\n");
+             if (h*hstepm/YEARM*stepm ==yearp) {
-         fprintf(ficparo,"\n");
+               fprintf(ficresf,"\n");
-         fprintf(ficlog,"\n");
+               for(j=1;j<=cptcoveff;j++)
-       }
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     }
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-     fflush(ficlog);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
-     delti=delti3[1][1];
+               ppij=0.;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                 else {
-     /* Reads comments: lines beginning with '#' */
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+                 }
-       ungetc(c,ficpar);
+                 if (h*hstepm/YEARM*stepm== yearp) {
-       fgets(line, MAXLINE, ficpar);
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-       numlinepar++;
+                 }
-       puts(line);
+               } /* end i */
-       fputs(line,ficparo);
+               if (h*hstepm/YEARM*stepm==yearp) {
-       fputs(line,ficlog);
+                 fprintf(ficresf," %.3f", ppij);
-     }
+               }
-     ungetc(c,ficpar);
+             }/* end j */
+           } /* end h */
-     matcov=matrix(1,npar,1,npar);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(i=1; i <=npar; i++){
+         } /* end agec */
-       fscanf(ficpar,"%s",&str);
+       } /* end yearp */
-       if(mle==1)
+     } /* end cptcod */
-         printf("%s",str);
+   } /* end  cptcov */
-       fprintf(ficlog,"%s",str);
-       fprintf(ficparo,"%s",str);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       for(j=1; j <=i; j++){
-         fscanf(ficpar," %le",&matcov[i][j]);
+   fclose(ficresf);
-         if(mle==1){
+ }
-           printf(" %.5le",matcov[i][j]);
-         }
+ /************** Forecasting *****not tested NB*************/
-         fprintf(ficlog," %.5le",matcov[i][j]);
+ 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(ficparo," %.5le",matcov[i][j]);
-       }
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-       fscanf(ficpar,"\n");
+   int *popage;
-       numlinepar++;
+   double calagedatem, agelim, kk1, kk2;
-       if(mle==1)
+   double *popeffectif,*popcount;
-         printf("\n");
+   double ***p3mat,***tabpop,***tabpopprev;
-       fprintf(ficlog,"\n");
+   double ***mobaverage;
-       fprintf(ficparo,"\n");
+   char filerespop[FILENAMELENGTH];
-     }
-     for(i=1; i <=npar; i++)
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       for(j=i+1;j<=npar;j++)
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         matcov[i][j]=matcov[j][i];
+   agelim=AGESUP;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-     if(mle==1)
-       printf("\n");
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     fprintf(ficlog,"\n");
-     fflush(ficlog);
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
-     /*-------- Rewriting parameter file ----------*/
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-     strcat(rfileres,".");    /* */
+   }
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     }
-     fprintf(ficres,"#%s\n",version);
+   if (mobilav!=0) {
-   }    /* End of mle != -3 */
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   /*-------- data file ----------*/
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   if((fic=fopen(datafile,"r"))==NULL)    {
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+     }
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   }
-   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   n= lastobs;
+   if (stepm<=12) stepsize=1;
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
+   agelim=AGESUP;
-   num=lvector(1,n);
-   moisnais=vector(1,n);
+   hstepm=1;
-   annais=vector(1,n);
+   hstepm=hstepm/stepm;
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+   if (popforecast==1) {
-   agedc=vector(1,n);
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-   cod=ivector(1,n);
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   weight=vector(1,n);
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+     }
-   mint=matrix(1,maxwav,1,n);
+     popage=ivector(0,AGESUP);
-   anint=matrix(1,maxwav,1,n);
+     popeffectif=vector(0,AGESUP);
-   s=imatrix(1,maxwav+1,1,n);
+     popcount=vector(0,AGESUP);
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   i=1;
-   linei=0;
+     imx=i;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-     linei=linei+1;
+   }
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-       if(line[j] == '\t')
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-         line[j] = ' ';
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-     }
+       k=k+1;
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       fprintf(ficrespop,"\n#******");
-       ;
+       for(j=1;j<=cptcoveff;j++) {
-     };
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     line[j+1]=0;  /* Trims blanks at end of line */
+       }
-     if(line[0]=='#'){
+       fprintf(ficrespop,"******\n");
-       fprintf(ficlog,"Comment line\n%s\n",line);
+       fprintf(ficrespop,"# Age");
-       printf("Comment line\n%s\n",line);
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-       continue;
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-     }
+       for (cpt=0; cpt<=0;cpt++) {
-     for (j=maxwav;j>=1;j--){
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-       cutv(stra, strb,line,' ');
-       errno=0;
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-       lval=strtol(strb,&endptr,10);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+           nhstepm = nhstepm/hstepm;
-       if( strb[0]=='\0' || (*endptr != '\0')){
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         exit(1);
+           oldm=oldms;savm=savms;
-       }
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-       s[j][i]=lval;
+           for (h=0; h<=nhstepm; h++){
-       strcpy(line,stra);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       cutv(stra, strb,line,' ');
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+             }
-       }
+             for(j=1; j<=nlstate+ndeath;j++) {
-       else  if(iout=sscanf(strb,"%s.") != 0){
+               kk1=0.;kk2=0;
-         month=99;
+               for(i=1; i<=nlstate;i++) {
-         year=9999;
+                 if (mobilav==1)
-       }else{
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-         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);
+                 else {
-         exit(1);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-       }
+                 }
-       anint[j][i]= (double) year;
+               }
-       mint[j][i]= (double)month;
+               if (h==(int)(calagedatem+12*cpt)){
-       strcpy(line,stra);
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-     } /* ENd Waves */
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-     cutv(stra, strb,line,' ');
+               }
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+             }
-     }
+             for(i=1; i<=nlstate;i++){
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+               kk1=0.;
-       month=99;
+                 for(j=1; j<=nlstate;j++){
-       year=9999;
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-     }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);
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-       exit(1);
+             }
-     }
-     andc[i]=(double) year;
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-     moisdc[i]=(double) month;
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-     strcpy(line,stra);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     cutv(stra, strb,line,' ');
+         }
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }
-     }
-     else  if(iout=sscanf(strb,"%s.") != 0){
+   /******/
-       month=99;
-       year=9999;
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-     }else{
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-       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 (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-       exit(1);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-     }
+           nhstepm = nhstepm/hstepm;
-     annais[i]=(double)(year);
-     moisnais[i]=(double)(month);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     strcpy(line,stra);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     cutv(stra, strb,line,' ');
+           for (h=0; h<=nhstepm; h++){
-     errno=0;
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-     dval=strtod(strb,&endptr);
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     if( strb[0]=='\0' || (*endptr != '\0')){
+             }
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+             for(j=1; j<=nlstate+ndeath;j++) {
-       exit(1);
+               kk1=0.;kk2=0;
-     }
+               for(i=1; i<=nlstate;i++) {
-     weight[i]=dval;
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-     strcpy(line,stra);
+               }
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-     for (j=ncovcol;j>=1;j--){
+             }
-       cutv(stra, strb,line,' ');
+           }
-       errno=0;
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       lval=strtol(strb,&endptr,10);
+         }
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       }
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+    }
-         exit(1);
+   }
-       }
-       if(lval <-1 || lval >1){
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         printf("Error reading data around '%d' at line number %ld 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 (popforecast==1) {
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+     free_ivector(popage,0,AGESUP);
-  For example, for multinomial values like 1, 2 and 3,\n \
+     free_vector(popeffectif,0,AGESUP);
-  build V1=0 V2=0 for the reference value (1),\n \
+     free_vector(popcount,0,AGESUP);
-         V1=1 V2=0 for (2) \n \
+   }
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  output of IMaCh is often meaningless.\n \
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  Exiting.\n",lval,linei, i,line,j);
+   fclose(ficrespop);
-         exit(1);
+ } /* End of popforecast */
-       }
-       covar[j][i]=(double)(lval);
+ int fileappend(FILE *fichier, char *optionfich)
-       strcpy(line,stra);
+ {
-     }
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-     lstra=strlen(stra);
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+     return (0);
-       stratrunc = &(stra[lstra-9]);
+   }
-       num[i]=atol(stratrunc);
+   fflush(fichier);
-     }
+   return (1);
-     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;}*/
+ /**************** function prwizard **********************/
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-     i=i+1;
+ {
-   } /* End loop reading  data */
-   fclose(fic);
+   /* Wizard to print covariance matrix template */
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
+   char ca[32], cb[32];
-   imx=i-1; /* Number of individuals */
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+   for(i=1; i <=nlstate; i++){
-     }*/
+     jj=0;
-    /*  for (i=1; i<=imx; i++){
+     for(j=1; j <=nlstate+ndeath; j++){
-      if (s[4][i]==9)  s[4][i]=-1;
+       if(j==i) continue;
-      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]));}*/
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   /* for (i=1; i<=imx; i++) */
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+       for(k=1; k<=ncovmodel;k++){
-      else weight[i]=1;*/
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-   /* Calculation of the number of parameters from char model */
+         printf(" 0.");
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+         fprintf(ficparo," 0.");
-   Tprod=ivector(1,15);
+       }
-   Tvaraff=ivector(1,15);
+       printf("\n");
-   Tvard=imatrix(1,15,1,2);
+       fprintf(ficparo,"\n");
-   Tage=ivector(1,15);
+     }
+   }
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+   printf("# Scales (for hessian or gradient estimation)\n");
-     j=0, j1=0, k1=1, k2=1;
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-     j=nbocc(model,'+'); /* j=Number of '+' */
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+   for(i=1; i <=nlstate; i++){
-     cptcovn=j+1;
+     jj=0;
-     cptcovprod=j1; /*Number of products */
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
-     strcpy(modelsav,model);
+       jj++;
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+       fprintf(ficparo,"%1d%1d",i,j);
-       printf("Error. Non available option model=%s ",model);
+       printf("%1d%1d",i,j);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       fflush(stdout);
-       goto end;
+       for(k=1; k<=ncovmodel;k++){
-     }
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-     /* This loop fills the array Tvar from the string 'model'.*/
+         printf(" 0.");
+         fprintf(ficparo," 0.");
-     for(i=(j+1); i>=1;i--){
+       }
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+       numlinepar++;
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       printf("\n");
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       fprintf(ficparo,"\n");
-       /*scanf("%d",i);*/
+     }
-       if (strchr(strb,'*')) {  /* Model includes a product */
+   }
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+   printf("# Covariance matrix\n");
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+ /* # 121 Var(a12)\n\ */
-           cptcovprod--;
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-           cutv(strb,stre,strd,'V');
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-           cptcovage++;
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-             Tage[cptcovage]=i;
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-             /*printf("stre=%s ", stre);*/
+ /* # 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" */
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+   fflush(stdout);
-           cptcovprod--;
+   fprintf(ficparo,"# Covariance matrix\n");
-           cutv(strb,stre,strc,'V');
+   /* # 121 Var(a12)\n\ */
-           Tvar[i]=atoi(stre);
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-           cptcovage++;
+   /* #   ...\n\ */
-           Tage[cptcovage]=i;
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-         }
-         else {  /* Age is not in the model */
+   for(itimes=1;itimes<=2;itimes++){
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+     jj=0;
-           Tvar[i]=ncovcol+k1;
+     for(i=1; i <=nlstate; i++){
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+       for(j=1; j <=nlstate+ndeath; j++){
-           Tprod[k1]=i;
+         if(j==i) continue;
-           Tvard[k1][1]=atoi(strc); /* m*/
+         for(k=1; k<=ncovmodel;k++){
-           Tvard[k1][2]=atoi(stre); /* n */
+           jj++;
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+           ca[0]= k+'a'-1;ca[1]='\0';
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+           if(itimes==1){
-           for (k=1; k<=lastobs;k++)
+             printf("#%1d%1d%d",i,j,k);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-           k1++;
+           }else{
-           k2=k2+2;
+             printf("%1d%1d%d",i,j,k);
-         }
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-       }
+             /*  printf(" %.5le",matcov[i][j]); */
-       else { /* no more sum */
+           }
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           ll=0;
-        /*  scanf("%d",i);*/
+           for(li=1;li <=nlstate; li++){
-       cutv(strd,strc,strb,'V');
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-       Tvar[i]=atoi(strc);
+               if(lj==li) continue;
-       }
+               for(lk=1;lk<=ncovmodel;lk++){
-       strcpy(modelsav,stra);
+                 ll++;
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+                 if(ll<=jj){
-         scanf("%d",i);*/
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-     } /* end of loop + */
+                   if(ll<jj){
-   } /* end model */
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+                     }else{
+                       printf(" 0.");
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+                       fprintf(ficparo," 0.");
-   printf("cptcovprod=%d ", cptcovprod);
+                     }
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+                   }else{
+                     if(itimes==1){
-   scanf("%d ",i);*/
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-     /*  if(mle==1){*/
+                     }else{
-   if (weightopt != 1) { /* Maximisation without weights*/
+                       printf(" 0.");
-     for(i=1;i<=n;i++) weight[i]=1.0;
+                       fprintf(ficparo," 0.");
-   }
+                     }
-     /*-calculation of age at interview from date of interview and age at death -*/
+                   }
-   agev=matrix(1,maxwav,1,imx);
+                 }
+               } /* end lk */
-   for (i=1; i<=imx; i++) {
+             } /* end lj */
-     for(m=2; (m<= maxwav); m++) {
+           } /* end li */
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+           printf("\n");
-         anint[m][i]=9999;
+           fprintf(ficparo,"\n");
-         s[m][i]=-1;
+           numlinepar++;
-       }
+         } /* end k*/
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+       } /*end j */
-         nberr++;
+     } /* end i */
-         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);
+   } /* end itimes */
-         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);
-         s[m][i]=-1;
+ } /* end of prwizard */
-       }
+ /******************* Gompertz Likelihood ******************************/
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+ double gompertz(double x[])
-         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]);
+   double A,B,L=0.0,sump=0.,num=0.;
-         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]);
+   int i,n=0; /* n is the size of the sample */
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       }
+   for (i=0;i<=imx-1 ; i++) {
-     }
+     sump=sump+weight[i];
-   }
+     /*    sump=sump+1;*/
+     num=num+1;
-   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]==-2 || s[m][i]==-4 || s[m][i]==-5){
+   /* for (i=0; i<=imx; i++)
-         if (s[m][i] >= nlstate+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]);*/
-           if(agedc[i]>0)
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+   for (i=1;i<=imx ; i++)
-               agev[m][i]=agedc[i];
+     {
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+       if (cens[i] == 1 && wav[i]>1)
-             else {
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-               if ((int)andc[i]!=9999){
-                 nbwarn++;
+       if (cens[i] == 0 && wav[i]>1)
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-                 agev[m][i]=-1;
-               }
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-             }
+       if (wav[i] > 1 ) { /* ??? */
-         }
+         L=L+A*weight[i];
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+         /*      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]);*/
-                                  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;
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-           else if(agev[m][i] <agemin){
-             agemin=agev[m][i];
+   return -2*L*num/sump;
-             /*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){
+ #ifdef GSL
-             agemax=agev[m][i];
+ /******************* Gompertz_f Likelihood ******************************/
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+ double gompertz_f(const gsl_vector *v, void *params)
-           }
+ {
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+   double A,B,LL=0.0,sump=0.,num=0.;
-           /*     agev[m][i] = age[i]+2*m;*/
+   double *x= (double *) v->data;
-         }
+   int i,n=0; /* n is the size of the sample */
-         else { /* =9 */
-           agev[m][i]=1;
+   for (i=0;i<=imx-1 ; i++) {
-           s[m][i]=-1;
+     sump=sump+weight[i];
-         }
+     /*    sump=sump+1;*/
-       }
+     num=num+1;
-       else /*= 0 Unknown */
+   }
-         agev[m][i]=1;
-     }
+   /* for (i=0; i<=imx; i++)
-   }
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   for (i=1; i<=imx; i++)  {
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     for(m=firstpass; (m<=lastpass); m++){
+   for (i=1;i<=imx ; i++)
-       if (s[m][i] > (nlstate+ndeath)) {
+     {
-         nberr++;
+       if (cens[i] == 1 && wav[i]>1)
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+       if (cens[i] == 0 && wav[i]>1)
-       }
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-     }
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-   }
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   /*for (i=1; i<=imx; i++){
+       if (wav[i] > 1 ) { /* ??? */
-   for (m=firstpass; (m<lastpass); m++){
+         LL=LL+A*weight[i];
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
- }
+       }
+     }
- }*/
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-   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 -2*LL*num/sump;
+ }
-   agegomp=(int)agemin;
+ #endif
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
+ /******************* Printing html file ***********/
-   free_vector(moisnais,1,n);
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   free_vector(annais,1,n);
+                   int lastpass, int stepm, int weightopt, char model[],\
-   /* free_matrix(mint,1,maxwav,1,n);
+                   int imx,  double p[],double **matcov,double agemortsup){
-      free_matrix(anint,1,maxwav,1,n);*/
+   int i,k;
-   free_vector(moisdc,1,n);
-   free_vector(andc,1,n);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
-   wav=ivector(1,imx);
+     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]));
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   fprintf(fichtm,"</ul>");
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   /* Concatenates waves */
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+  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>");
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+  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]);
-   Tcode=ivector(1,100);
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-   ncodemax[1]=1;
+   fflush(fichtm);
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+ }
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+ /******************* Gnuplot file **************/
-                                  the estimations*/
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   h=0;
-   m=pow(2,cptcoveff);
+   char dirfileres[132],optfileres[132];
-   for(k=1;k<=cptcoveff; k++){
+   int ng;
-     for(i=1; i <=(m/pow(2,k));i++){
-       for(j=1; j <= ncodemax[k]; j++){
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   /*#ifdef windows */
-           h++;
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+     /*#endif */
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
-         }
-       }
+   strcpy(dirfileres,optionfilefiname);
-     }
+   strcpy(optfileres,"vpl");
-   }
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-      codtab[1][2]=1;codtab[2][2]=2; */
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-   /* for(i=1; i <=m ;i++){
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-      for(k=1; k <=cptcovn; k++){
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-      }
+ }
-      printf("\n");
-      }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-      scanf("%d",i);*/
+ {
-   /*------------ gnuplot -------------*/
+   /*-------- data file ----------*/
-   strcpy(optionfilegnuplot,optionfilefiname);
+   FILE *fic;
-   if(mle==-3)
+   char dummy[]="                         ";
-     strcat(optionfilegnuplot,"-mort");
+   int i=0, j=0, n=0;
-   strcat(optionfilegnuplot,".gp");
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   char stra[MAXLINE], strb[MAXLINE];
-     printf("Problem with file %s",optionfilegnuplot);
+   char *stratrunc;
-   }
+   int lstra;
-   else{
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     fprintf(ficgp,"set missing 'NaNq'\n");
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-   }
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-   /*  fclose(ficgp);*/
+   }
-   /*--------- index.htm --------*/
+   i=1;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   linei=0;
-   if(mle==-3)
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     strcat(optionfilehtm,"-mort");
+     linei=linei+1;
-   strcat(optionfilehtm,".htm");
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+       if(line[j] == '\t')
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+         line[j] = ' ';
-   }
+     }
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+       ;
-   strcat(optionfilehtmcov,"-cov.htm");
+     };
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     line[j+1]=0;  /* Trims blanks at end of line */
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+     if(line[0]=='#'){
-   }
+       fprintf(ficlog,"Comment line\n%s\n",line);
-   else{
+       printf("Comment line\n%s\n",line);
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+       continue;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     }
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+     strcpy(line, linetmp);
-   }
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     for (j=maxwav;j>=1;j--){
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+       cutv(stra, strb, line, ' ');
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+       if(strb[0]=='.') { /* Missing status */
- \n\
+         lval=-1;
- <hr  size=\"2\" color=\"#EC5E5E\">\
+       }else{
-  <ul><li><h4>Parameter files</h4>\n\
+         errno=0;
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+         lval=strtol(strb,&endptr,10);
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+         if( strb[0]=='\0' || (*endptr != '\0')){
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+           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);
-  - Date and time at start: %s</ul>\n",\
+           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);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           return 1;
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+         }
-           fileres,fileres,\
+       }
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+       s[j][i]=lval;
-   fflush(fichtm);
+       strcpy(line,stra);
-   strcpy(pathr,path);
+       cutv(stra, strb,line,' ');
-   strcat(pathr,optionfilefiname);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+       }
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+         month=99;
-      and prints on file fileres'p'. */
+         year=9999;
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-   fprintf(fichtm,"\n");
+         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);
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         return 1;
- 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",\
+       anint[j][i]= (double) year;
-           imx,agemin,agemax,jmin,jmax,jmean);
+       mint[j][i]= (double)month;
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       strcpy(line,stra);
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     } /* ENd Waves */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     cutv(stra, strb,line,' ');
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       month=99;
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+       year=9999;
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+     }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);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
-   if (mle==-3){
+     }
-     ximort=matrix(1,NDIM,1,NDIM);
+     andc[i]=(double) year;
-     cens=ivector(1,n);
+     moisdc[i]=(double) month;
-     ageexmed=vector(1,n);
+     strcpy(line,stra);
-     agecens=vector(1,n);
-     dcwave=ivector(1,n);
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-     for (i=1; i<=imx; i++){
+     }
-       dcwave[i]=-1;
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-       for (m=firstpass; m<=lastpass; m++)
+       month=99;
-         if (s[m][i]>nlstate) {
+       year=9999;
-           dcwave[i]=m;
+     }else{
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+       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);
-           break;
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-         }
+         return 1;
      }
+     if (year==9999) {
-     for (i=1; i<=imx; i++) {
+       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);
-       if (wav[i]>0){
+       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);
-         ageexmed[i]=agev[mw[1][i]][i];
+         return 1;
-         j=wav[i];
-         agecens[i]=1.;
+     }
+     annais[i]=(double)(year);
-         if (ageexmed[i]> 1 && wav[i] > 0){
+     moisnais[i]=(double)(month);
-           agecens[i]=agev[mw[j][i]][i];
+     strcpy(line,stra);
-           cens[i]= 1;
-         }else if (ageexmed[i]< 1)
+     cutv(stra, strb,line,' ');
-           cens[i]= -1;
+     errno=0;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+     dval=strtod(strb,&endptr);
-           cens[i]=0 ;
+     if( strb[0]=='\0' || (*endptr != '\0')){
-       }
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       else cens[i]=-1;
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-     }
+       fflush(ficlog);
+       return 1;
-     for (i=1;i<=NDIM;i++) {
+     }
-       for (j=1;j<=NDIM;j++)
+     weight[i]=dval;
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     strcpy(line,stra);
-     }
+     for (j=ncovcol;j>=1;j--){
-     p[1]=0.0268; p[NDIM]=0.083;
+       cutv(stra, strb,line,' ');
-     /*printf("%lf %lf", p[1], p[2]);*/
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         errno=0;
-     strcpy(filerespow,"pow-mort");
+         lval=strtol(strb,&endptr,10);
-     strcat(filerespow,fileres);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+           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);
-       printf("Problem with resultfile: %s\n", filerespow);
+           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);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+           return 1;
-     }
+         }
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+       }
-     /*  for (i=1;i<=nlstate;i++)
+       if(lval <-1 || lval >1){
-         for(j=1;j<=nlstate+ndeath;j++)
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     fprintf(ficrespow,"\n");
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+         V1=1 V2=0 for (2) \n \
-     fclose(ficrespow);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+  Exiting.\n",lval,linei, i,line,j);
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     for(i=1; i <=NDIM; i++)
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-       for(j=i+1;j<=NDIM;j++)
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-         matcov[i][j]=matcov[j][i];
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
-     printf("\nCovariance matrix\n ");
+         V1=1 V2=0 for (2) \n \
-     for(i=1; i <=NDIM; i++) {
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       for(j=1;j<=NDIM;j++){
+  output of IMaCh is often meaningless.\n \
-         printf("%f ",matcov[i][j]);
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       }
+         return 1;
-       printf("\n ");
+       }
-     }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
-     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++)
+     lstra=strlen(stra);
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-     lsurv=vector(1,AGESUP);
+       stratrunc = &(stra[lstra-9]);
-     lpop=vector(1,AGESUP);
+       num[i]=atol(stratrunc);
-     tpop=vector(1,AGESUP);
+     }
-     lsurv[agegomp]=100000;
+     else
+       num[i]=atol(stra);
-     for (k=agegomp;k<=AGESUP;k++) {
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       agemortsup=k;
+       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 (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     }
+     i=i+1;
+   } /* End loop reading  data */
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
-     for (k=agegomp;k<agemortsup;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   return (0);
-       sumlpop=sumlpop+lpop[k];
+   /* endread: */
-     }
+     printf("Exiting readdata: ");
+     fclose(fic);
-     tpop[agegomp]=sumlpop;
+     return (1);
-     for (k=agegomp;k<(agemortsup-3);k++){
-       /*  tpop[k+1]=2;*/
-       tpop[k+1]=tpop[k]-lpop[k];
-     }
+ }
+ void removespace(char *str) {
+   char *p1 = str, *p2 = str;
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   do
-     for (k=agegomp;k<(agemortsup-2);k++)
+     while (*p2 == ' ')
-       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]);
+       p2++;
+   while (*p1++ == *p2++);
+ }
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ 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
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+    * - nagesqr = 1 if age*age in the model, otherwise 0.
-                      stepm, weightopt,\
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
-                      model,imx,p,matcov,agemortsup);
+    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+    * - cptcovage number of covariates with age*products =2
-     free_vector(lsurv,1,AGESUP);
+    * - cptcovs number of simple covariates
-     free_vector(lpop,1,AGESUP);
+    * - 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
-     free_vector(tpop,1,AGESUP);
+    *     which is a new column after the 9 (ncovcol) variables.
-   } /* Endof if mle==-3 */
+    * - 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
-   else{ /* For mle >=1 */
+    *    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 .
-     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++)
+   int i, j, k, ks;
-       printf(" %d %8.5f",k,p[k]);
+   int  j1, k1, k2;
-     printf("\n");
+   char modelsav[80];
-     globpr=1; /* to print the contributions */
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   char *strpt;
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+   /*removespace(model);*/
-       printf(" %d %8.5f",k,p[k]);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-     printf("\n");
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     if(mle>=1){ /* Could be 1 or 2 */
+     if (strstr(model,"AGE") !=0){
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+       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;
-     /*--------- results files --------------*/
+     }
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     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);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       return 1;
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     }
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     strcpy(modelsav,model);
-     for(i=1,jk=1; i <=nlstate; i++){
+     if ((strpt=strstr(model,"age*age")) !=0){
-       for(k=1; k <=(nlstate+ndeath); k++){
+       printf(" strpt=%s, model=%s\n",strpt, model);
-         if (k != i) {
+       if(strpt != model){
-           printf("%d%d ",i,k);
+       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-           fprintf(ficlog,"%d%d ",i,k);
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-           fprintf(ficres,"%1d%1d ",i,k);
+  corresponding column of parameters.\n",model);
-           for(j=1; j <=ncovmodel; j++){
+       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-             printf("%lf ",p[jk]);
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-             fprintf(ficlog,"%lf ",p[jk]);
+  corresponding column of parameters.\n",model); fflush(ficlog);
-             fprintf(ficres,"%lf ",p[jk]);
+       return 1;
-             jk++;
+     }
-           }
-           printf("\n");
+       nagesqr=1;
-           fprintf(ficlog,"\n");
+       if (strstr(model,"+age*age") !=0)
-           fprintf(ficres,"\n");
+         substrchaine(modelsav, model, "+age*age");
-         }
+       else if (strstr(model,"age*age+") !=0)
-       }
+         substrchaine(modelsav, model, "age*age+");
-     }
+       else
-     if(mle!=0){
+         substrchaine(modelsav, model, "age*age");
-       /* Computing hessian and covariance matrix */
+     }else
-       ftolhess=ftol; /* Usually correct */
+       nagesqr=0;
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+     if (strlen(modelsav) >1){
-     }
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-     printf("# Scales (for hessian or gradient estimation)\n");
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-     for(i=1,jk=1; i <=nlstate; i++){
+                    * cst, age and age*age
-       for(j=1; j <=nlstate+ndeath; j++){
+                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
-         if (j!=i) {
+                   /* including age products which are counted in cptcovage.
-           fprintf(ficres,"%1d%1d",i,j);
+                   * but the covariates which are products must be treated
-           printf("%1d%1d",i,j);
+                   * separately: ncovn=4- 2=2 (V1+V3). */
-           fprintf(ficlog,"%1d%1d",i,j);
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-           for(k=1; k<=ncovmodel;k++){
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-             printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
-             fprintf(ficres," %.5e",delti[jk]);
+       /*   Design
-             jk++;
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-           }
+        *  <          ncovcol=8                >
-           printf("\n");
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-           fprintf(ficlog,"\n");
+        *   k=  1    2      3       4     5       6      7        8
-           fprintf(ficres,"\n");
+        *  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
-     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");
+        *  Tage[++cptcovage]=k
-     if(mle>=1)
+        *       if products, new covar are created after ncovcol with k1
-       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");
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-     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");
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-     /* # 121 Var(a12)\n\ */
+        *  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
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+        *  <          ncovcol=8                >
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+        *     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}
-     /* Just to have a covariance matrix which will be more understandable
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
-        even is we still don't want to manage dictionary of variables
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-     */
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     for(itimes=1;itimes<=2;itimes++){
+        *How to reorganize?
-       jj=0;
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-       for(i=1; i <=nlstate; i++){
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         for(j=1; j <=nlstate+ndeath; j++){
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
-           if(j==i) continue;
+        * Struct []
-           for(k=1; k<=ncovmodel;k++){
+        */
-             jj++;
-             ca[0]= k+'a'-1;ca[1]='\0';
+       /* This loop fills the array Tvar from the string 'model'.*/
-             if(itimes==1){
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-               if(mle>=1)
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-                 printf("#%1d%1d%d",i,j,k);
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
-             }else{
+       /*        k=1 Tvar[1]=2 (from V2) */
-               if(mle>=1)
+       /*        k=5 Tvar[5] */
-                 printf("%1d%1d%d",i,j,k);
+       /* for (k=1; k<=cptcovn;k++) { */
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+       /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+       /*        } */
-             }
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
-             ll=0;
+       /*
-             for(li=1;li <=nlstate; li++){
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-                 if(lj==li) continue;
+         Tvar[k]=0;
-                 for(lk=1;lk<=ncovmodel;lk++){
+       cptcovage=0;
-                   ll++;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-                   if(ll<=jj){
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-                     if(ll<jj){
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-                       if(itimes==1){
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-                         if(mle>=1)
+         /*scanf("%d",i);*/
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-                       }else{
+             /* covar is not filled and then is empty */
-                         if(mle>=1)
+             cptcovprod--;
-                           printf(" %.5e",matcov[jj][ll]);
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+             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 */
-                     }else{
+             /*printf("stre=%s ", stre);*/
-                       if(itimes==1){
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-                         if(mle>=1)
+             cptcovprod--;
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+             cutl(stre,strb,strc,'V');
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+             Tvar[k]=atoi(stre);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+             cptcovage++;
-                       }else{
+             Tage[cptcovage]=k;
-                         if(mle>=1)
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-                           printf(" %.5e",matcov[jj][ll]);
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+             cptcovn++;
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+             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
-                 } /* end lk */
+                                    ncovcol + k1
-               } /* end lj */
+                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-             } /* end li */
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-             if(mle>=1)
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-               printf("\n");
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-             fprintf(ficlog,"\n");
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-             fprintf(ficres,"\n");
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-             numlinepar++;
+             k2=k2+2;
-           } /* end k*/
+             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-         } /*end j */
+             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-       } /* end i */
+             for (i=1; i<=lastobs;i++){
-     } /* end itimes */
+               /* 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 */
-     fflush(ficlog);
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-     fflush(ficres);
+             }
+           } /* End age is not in the model */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         } /* End if model includes a product */
-       ungetc(c,ficpar);
+         else { /* no more sum */
-       fgets(line, MAXLINE, ficpar);
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       puts(line);
+           /*  scanf("%d",i);*/
-       fputs(line,ficparo);
+           cutl(strd,strc,strb,'V');
-     }
+           ks++; /**< Number of simple covariates */
-     ungetc(c,ficpar);
+           cptcovn++;
+           Tvar[k]=atoi(strd);
-     estepm=0;
+         }
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-     if (fage <= 2) {
+           scanf("%d",i);*/
-       bage = ageminpar;
+       } /* end of loop + on total covariates */
-       fage = agemaxpar;
+     } /* end if strlen(modelsave == 0) age*age might exist */
-     }
+   } /* end if strlen(model == 0) */
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\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.
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   printf("cptcovprod=%d ", cptcovprod);
-       ungetc(c,ficpar);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+   scanf("%d ",i);*/
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
+   /*endread:*/
-     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);
+     printf("Exiting decodemodel: ");
-     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);
+     return (1);
-     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);
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   int i, m;
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   for (i=1; i<=imx; i++) {
-       puts(line);
+     for(m=2; (m<= maxwav); m++) {
-       fputs(line,ficparo);
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-     }
+         anint[m][i]=9999;
-     ungetc(c,ficpar);
+         s[m][i]=-1;
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+         *nberr = *nberr + 1;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+         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);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+         s[m][i]=-1;
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+       }
-     fprintf(ficres,"pop_based=%d\n",popbased);
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         (*nberr)++;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         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]);
-       ungetc(c,ficpar);
+         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]);
-       fgets(line, MAXLINE, ficpar);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       puts(line);
+       }
-       fputs(line,ficparo);
+     }
-     }
+   }
-     ungetc(c,ficpar);
+   for (i=1; i<=imx; i++)  {
-     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);
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     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);
+     for(m=firstpass; (m<= lastpass); m++){
-     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);
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-     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);
+         if (s[m][i] >= nlstate+1) {
-     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);
+           if(agedc[i]>0){
-     /* day and month of proj2 are not used but only year anproj2.*/
+             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 {
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+               if ((int)andc[i]!=9999){
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 agev[m][i]=-1;
+               }
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+             }
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+           } /* agedc > 0 */
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+         }
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-    /*------------ free_vector  -------------*/
+                                  years but with the precision of a month */
-    /*  chdir(path); */
+           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)
-     free_ivector(wav,1,imx);
+             agev[m][i]=1;
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+           else if(agev[m][i] < *agemin){
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+             *agemin=agev[m][i];
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-     free_lvector(num,1,n);
+           }
-     free_vector(agedc,1,n);
+           else if(agev[m][i] >*agemax){
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+             *agemax=agev[m][i];
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-     fclose(ficparo);
+           }
-     fclose(ficres);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
+         }
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+         else { /* =9 */
+           agev[m][i]=1;
-     strcpy(filerespl,"pl");
+           s[m][i]=-1;
-     strcat(filerespl,fileres);
+         }
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+       }
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+       else /*= 0 Unknown */
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+         agev[m][i]=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);
+   for (i=1; i<=imx; i++)  {
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     for(m=firstpass; (m<=lastpass); m++){
-     fprintf(ficrespl,"#Age ");
+       if (s[m][i] > (nlstate+ndeath)) {
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+         (*nberr)++;
-     fprintf(ficrespl,"\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);
+         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);
-     prlim=matrix(1,nlstate,1,nlstate);
+         return 1;
+       }
-     agebase=ageminpar;
+     }
-     agelim=agemaxpar;
+   }
-     ftolpl=1.e-10;
-     i1=cptcoveff;
+   /*for (i=1; i<=imx; i++){
-     if (cptcovn < 1){i1=1;}
+   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]);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ }
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+ }*/
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         fprintf(ficlog,"\n#******");
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   return (0);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  /* endread:*/
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     printf("Exiting calandcheckages: ");
-         }
+     return (1);
-         fprintf(ficrespl,"******\n");
+ }
-         printf("******\n");
-         fprintf(ficlog,"******\n");
+ #if defined(_MSC_VER)
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-         for (age=agebase; age<=agelim; age++){
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+ //#include "stdafx.h"
-           fprintf(ficrespl,"%.0f ",age );
+ //#include <stdio.h>
-           for(j=1;j<=cptcoveff;j++)
+ //#include <tchar.h>
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ //#include <windows.h>
-           for(i=1; i<=nlstate;i++)
+ //#include <iostream>
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
-           fprintf(ficrespl,"\n");
-         }
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
-       }
-     }
+ BOOL IsWow64()
-     fclose(ficrespl);
+ {
+         BOOL bIsWow64 = FALSE;
-     /*------------- h Pij x at various ages ------------*/
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+         //  (HANDLE, PBOOL);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
+         HMODULE module = GetModuleHandle(_T("kernel32"));
-     printf("Computing pij: result on file '%s' \n", filerespij);
+         const char funcName[] = "IsWow64Process";
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
+                 GetProcAddress(module, funcName);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
-     /*if (stepm<=24) stepsize=2;*/
+         if (NULL != fnIsWow64Process)
+         {
-     agelim=AGESUP;
+                 if (!fnIsWow64Process(GetCurrentProcess(),
-     hstepm=stepsize*YEARM; /* Every year of age */
+                         &bIsWow64))
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+                         //throw std::exception("Unknown error");
+                         printf("Unknown error\n");
-     /* hstepm=1;   aff par mois*/
+         }
-     pstamp(ficrespij);
+         return bIsWow64 != FALSE;
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+ }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ #endif
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+ void syscompilerinfo(int logged)
-         fprintf(ficrespij,"\n#****** ");
+  {
-         for(j=1;j<=cptcoveff;j++)
+    /* #include "syscompilerinfo.h"*/
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    /* command line Intel compiler 32bit windows, XP compatible:*/
-         fprintf(ficrespij,"******\n");
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+    /* 64 bits */
+    /*
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      /GS /W3 /Gy
-           oldm=oldms;savm=savms;
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
-           for(i=1; i<=nlstate;i++)
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
-             for(j=1; j<=nlstate+ndeath;j++)
+    /* Optimization are useless and O3 is slower than O2 */
-               fprintf(ficrespij," %1d-%1d",i,j);
+    /*
-           fprintf(ficrespij,"\n");
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
-           for (h=0; h<=nhstepm; h++){
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
-             for(i=1; i<=nlstate;i++)
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
-               for(j=1; j<=nlstate+ndeath;j++)
+    */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+    /* Link is */ /* /OUT:"visual studio
-             fprintf(ficrespij,"\n");
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
-           }
+       /PDB:"visual studio
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
-           fprintf(ficrespij,"\n");
+       "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'
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
-     fclose(ficrespij);
+       /NOLOGO /TLBID:1
+    */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ #if defined __INTEL_COMPILER
-     for(i=1;i<=AGESUP;i++)
+ #if defined(__GNUC__)
-       for(j=1;j<=NCOVMAX;j++)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
-         for(k=1;k<=NCOVMAX;k++)
+ #endif
-           probs[i][j][k]=0.;
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
-     /*---------- Forecasting ------------------*/
+ #include <gnu/libc-version.h>  /* Only on gnu */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+ #endif
-     if(prevfcast==1){
+    struct utsname sysInfo;
-       /*    if(stepm ==1){*/
+    int cross = CROSS;
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+    if (cross){
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+            printf("Cross-");
-       /*      }  */
+            if(logged) fprintf(ficlog, "Cross-");
-       /*      else{ */
+    }
-       /*        erreur=108; */
+ #endif
-       /*        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); */
+ #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. ---------------------------------------------- */
-     /*---------- Health expectancies and variances ------------*/
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
-     strcpy(filerest,"t");
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
-     strcat(filerest,fileres);
+ #endif
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+ #if defined(__GNUC__) || defined(__GNUG__)
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+ #endif
-     }
+ #if defined(__HP_cc) || defined(__HP_aCC)
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
-     strcpy(filerese,"e");
+ #endif
-     strcat(filerese,fileres);
+ #if defined(_MSC_VER)
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+ #endif
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+ #if defined(__PGI)
-     }
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+ #endif
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
-     strcpy(fileresstde,"stde");
+ #endif
-     strcat(fileresstde,fileres);
+    printf(" for "); if (logged) fprintf(ficlog, " for ");
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
-     }
+     // Windows (x64 and x86)
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ #elif __unix__ // all unices, not all compilers
+     // Unix
-     strcpy(filerescve,"cve");
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
-     strcat(filerescve,fileres);
+ #elif __linux__
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+     // linux
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ #elif __APPLE__
-     }
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ #endif
-     strcpy(fileresv,"v");
+ /*  __MINGW32__   */
-     strcat(fileresv,fileres);
+ /*  __CYGWIN__   */
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+ /* __MINGW64__  */
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+ /* _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 */
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ /* _WIN64  // Defined for applications for Win64. */
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ /* _M_X64 // Defined for compilations that target x64 processors. */
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
-     /* 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);
+ #if UINTPTR_MAX == 0xffffffff
-     /*  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",\
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+ #elif UINTPTR_MAX == 0xffffffffffffffff
-     */
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
-     if (mobilav!=0) {
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ #endif
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ #if defined(__GNUC__)
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ # if defined(__GNUC_PATCHLEVEL__)
-       }
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     }
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ # else
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-         k=k+1;
+                             + __GNUC_MINOR__ * 100)
-         fprintf(ficrest,"\n#****** ");
+ # endif
-         for(j=1;j<=cptcoveff;j++)
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
-         fprintf(ficrest,"******\n");
+    if (uname(&sysInfo) != -1) {
-         fprintf(ficreseij,"\n#****** ");
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-         fprintf(ficresstdeij,"\n#****** ");
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-         fprintf(ficrescveij,"\n#****** ");
+    }
-         for(j=1;j<=cptcoveff;j++) {
+    else
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       perror("uname() error");
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+    //#ifndef __INTEL_COMPILER
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
-         }
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
-         fprintf(ficreseij,"******\n");
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
-         fprintf(ficresstdeij,"******\n");
+ #endif
-         fprintf(ficrescveij,"******\n");
+ #endif
-         fprintf(ficresvij,"\n#****** ");
+    //   void main()
-         for(j=1;j<=cptcoveff;j++)
+    //   {
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ #if defined(_MSC_VER)
-         fprintf(ficresvij,"******\n");
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-         oldm=oldms;savm=savms;
+    }
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+    else{
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+            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");
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+    }
-         oldm=oldms;savm=savms;
+    //      printf("\nPress Enter to continue...");
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+    //      getchar();
-         if(popbased==1){
+    //   }
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-         }
+ #endif
-         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) ");
+  }
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-         fprintf(ficrest,"\n");
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-         epj=vector(1,nlstate+1);
+   int i, j, k, i1 ;
-         for(age=bage; age <=fage ;age++){
+   double ftolpl = 1.e-10;
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   double age, agebase, agelim;
-           if (popbased==1) {
-             if(mobilav ==0){
+     strcpy(filerespl,"pl");
-               for(i=1; i<=nlstate;i++)
+     strcat(filerespl,fileres);
-                 prlim[i][i]=probs[(int)age][i][k];
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-             }else{ /* mobilav */
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-               for(i=1; i<=nlstate;i++)
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     }
-             }
+     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(ficrest," %4.0f",age);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     fprintf(ficrespl,"#Age ");
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     fprintf(ficrespl,"\n");
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-             }
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
-             epj[nlstate+1] +=epj[j];
-           }
+     agebase=ageminpar;
+     agelim=agemaxpar;
-           for(i=1, vepp=0.;i <=nlstate;i++)
-             for(j=1;j <=nlstate;j++)
+     i1=pow(2,cptcoveff);
-               vepp += vareij[i][j][(int)age];
+     if (cptcovn < 1){i1=1;}
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-           for(j=1;j <=nlstate;j++){
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-           }
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-           fprintf(ficrest,"\n");
+         k=k+1;
-         }
+         /* to clean */
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         fprintf(ficrespl,"\n#******");
-         free_vector(epj,1,nlstate+1);
+         printf("\n#******");
-       }
+         fprintf(ficlog,"\n#******");
-     }
+         for(j=1;j<=cptcoveff;j++) {
-     free_vector(weight,1,n);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     free_imatrix(Tvard,1,15,1,2);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     free_imatrix(s,1,maxwav+1,1,n);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     free_matrix(anint,1,maxwav,1,n);
+         }
-     free_matrix(mint,1,maxwav,1,n);
+         fprintf(ficrespl,"******\n");
-     free_ivector(cod,1,n);
+         printf("******\n");
-     free_ivector(tab,1,NCOVMAX);
+         fprintf(ficlog,"******\n");
-     fclose(ficreseij);
-     fclose(ficresstdeij);
+         fprintf(ficrespl,"#Age ");
-     fclose(ficrescveij);
+         for(j=1;j<=cptcoveff;j++) {
-     fclose(ficresvij);
+           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     fclose(ficrest);
+         }
-     fclose(ficpar);
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+         fprintf(ficrespl,"\n");
-     /*------- Variance of period (stable) prevalence------*/
+         for (age=agebase; age<=agelim; age++){
-     strcpy(fileresvpl,"vpl");
+         /* for (age=agebase; age<=agebase; age++){ */
-     strcat(fileresvpl,fileres);
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+           fprintf(ficrespl,"%.0f ",age );
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+           for(j=1;j<=cptcoveff;j++)
-       exit(0);
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     }
+           for(i=1; i<=nlstate;i++)
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl,"\n");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         } /* Age */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         /* was end of cptcod */
-         k=k+1;
+     } /* cptcov */
-         fprintf(ficresvpl,"\n#****** ");
+         return 0;
-         for(j=1;j<=cptcoveff;j++)
+ }
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+   int stepsize;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+   int agelim;
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+   int hstepm;
-       }
+   int nhstepm;
-     }
+   int h, i, i1, j, k;
-     fclose(ficresvpl);
+   double agedeb;
+   double ***p3mat;
-     /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
-   }  /* mle==-3 arrives here for freeing */
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     }
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     printf("Computing pij: result on file '%s' \n", filerespij);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-     free_matrix(covar,0,NCOVMAX,1,n);
+     /*if (stepm<=24) stepsize=2;*/
-     free_matrix(matcov,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+     agelim=AGESUP;
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     hstepm=stepsize*YEARM; /* Every year of age */
-     free_matrix(agev,1,maxwav,1,imx);
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     /* hstepm=1;   aff par mois*/
-     free_ivector(ncodemax,1,8);
+     pstamp(ficrespij);
-     free_ivector(Tvar,1,15);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     free_ivector(Tprod,1,15);
+     i1= pow(2,cptcoveff);
-     free_ivector(Tvaraff,1,15);
+    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     free_ivector(Tage,1,15);
+    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
-     free_ivector(Tcode,1,100);
+    /*   k=k+1;  */
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+       fprintf(ficrespij,"\n#****** ");
-     free_imatrix(codtab,1,100,1,10);
+       for(j=1;j<=cptcoveff;j++)
-   fflush(fichtm);
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   fflush(ficgp);
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-   if((nberr >0) || (nbwarn>0)){
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
-   }else{
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-     printf("End of Imach\n");
-     fprintf(ficlog,"End of Imach\n");
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
+         oldm=oldms;savm=savms;
-   printf("See log file on %s\n",filelog);
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-   (void) gettimeofday(&end_time,&tzp);
+         for(i=1; i<=nlstate;i++)
-   tm = *localtime(&end_time.tv_sec);
+           for(j=1; j<=nlstate+ndeath;j++)
-   tmg = *gmtime(&end_time.tv_sec);
+             fprintf(ficrespij," %1d-%1d",i,j);
-   strcpy(strtend,asctime(&tm));
+         fprintf(ficrespij,"\n");
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+         for (h=0; h<=nhstepm; h++){
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+             for(j=1; j<=nlstate+ndeath;j++)
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+           fprintf(ficrespij,"\n");
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+         }
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+         fprintf(ficrespij,"\n");
-   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);
+         return 0;
-   fclose(ficlog);
+ }
-   /*------ End -----------*/
+ /***********************************************/
-    printf("Before Current directory %s!\n",pathcd);
+ /**************** Main Program *****************/
-    if(chdir(pathcd) != 0)
+ /***********************************************/
-     printf("Can't move to directory %s!\n",path);
-   if(getcwd(pathcd,MAXLINE) > 0)
+ int main(int argc, char *argv[])
-     printf("Current directory %s!\n",pathcd);
+ {
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+ #ifdef GSL
-   sprintf(plotcmd,"gnuplot");
+   const gsl_multimin_fminimizer_type *T;
- #ifndef UNIX
+   size_t iteri = 0, it;
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+   int rval = GSL_CONTINUE;
- #endif
+   int status = GSL_SUCCESS;
-   if(!stat(plotcmd,&info)){
+   double ssval;
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ #endif
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     }else
-       strcpy(pplotcmd,plotcmd);
+   int jj, ll, li, lj, lk;
- #ifdef UNIX
+   int numlinepar=0; /* Current linenumber of parameter file */
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+   int itimes;
-     if(!stat(plotcmd,&info)){
+   int NDIM=2;
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+   int vpopbased=0;
-     }else
-       strcpy(pplotcmd,plotcmd);
+   char ca[32], cb[32];
- #endif
+   /*  FILE *fichtm; *//* Html File */
-   }else
+   /* FILE *ficgp;*/ /*Gnuplot File */
-     strcpy(pplotcmd,plotcmd);
+   struct stat info;
+   double agedeb=0.;
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+   double fret;
-   if((outcmd=system(plotcmd)) != 0){
+   double dum=0.; /* Dummy variable */
-     printf("\n Problem with gnuplot\n");
+   double ***p3mat;
-   }
+   double ***mobaverage;
-   printf(" Wait...");
-   while (z[0] != 'q') {
+   char line[MAXLINE];
-     /* chdir(path); */
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+   char pathr[MAXLINE], pathimach[MAXLINE];
-     scanf("%s",z);
+   char *tok, *val; /* pathtot */
- /*     if (z[0] == 'c') system("./imach"); */
+   int firstobs=1, lastobs=10;
-     if (z[0] == 'e') {
+   int c,  h , cpt;
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+   int jl=0;
-       system(optionfilehtm);
+   int i1, j1, jk, stepsize=0;
-     }
+   int *tab;
-     else if (z[0] == 'g') system(plotcmd);
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     else if (z[0] == 'q') exit(0);
+   int mobilav=0,popforecast=0;
-   }
+   int hstepm=0, nhstepm=0;
-   end:
+   int agemortsup;
-   while (z[0] != 'q') {
+   float  sumlpop=0.;
-     printf("\nType  q for exiting: ");
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     scanf("%s",z);
+   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 ***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("\n%s\n%s",version,fullversion);
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+     i=strlen(pathr);
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+    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,"\n%s\n%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(0);
+   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(fileres,".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,fileres);
+   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;
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
+     fputs(line,stdout);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"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++;
+   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);
+   if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
+     model[strlen(model)-1]='\0';
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=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++;
+     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);
+   }
+   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);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
+       if(mle==1)
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
+       fprintf(ficparo,"%s",str);
+       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");
+     }
+     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", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);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);
+   /* Concatenates waves */
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
+   /* 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 of jth covariate, in
+      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
+   /* 1 to ncodemax[j] 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],codtab[100][10]);*/
+   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
+   h=0;
+   /*if (cptcovn > 0) */
+   m=pow(2,cptcoveff);
+   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)  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 2**k
+            * codtabm(h,k)=  1 & (h-1) >> (k-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     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     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# %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=%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %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=%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);
+   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,fileres);
+     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, 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 ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\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 / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,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 maximisation */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     /* Computes likelihood for initial parameters */
+     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");
+     globpr=1; /* again, to print the contributions */
+     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");
+     if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- 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 */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     printf("Parameters and 95%% confidence intervals\n");
+     fprintf(ficlog, "Parameters, T and confidence intervals\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 T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+             fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+         }
+       }
+     }
+     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)
+       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(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",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((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     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\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     /* 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 / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     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);
+     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);
+     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(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      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);
+     */
+     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,fileres);
+     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' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*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]][codtab[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);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     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);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     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,fileres);
+     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,fileres);
+     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' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*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]][codtab[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]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* 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; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,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 e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             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",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];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             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");
+           }
+         }
+         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);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     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' \n", fileresvpl);
+     /*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]][codtab[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,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- 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_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: ");
+     scanf("%s",z);
+   }
+ }

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