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Diff for /imach/src/imach.c between versions 1.125 and 1.206

-version 1.125, 2006/04/04 15:20:31
+version 1.206, 2015/10/24 07:14:11
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.206  2015/10/24 07:14:11  brouard
+   *** empty log message ***
+   Revision 1.205  2015/10/23 15:50:53  brouard
+   Summary: 0.98r3 some clarification for graphs on likelihood contributions
+   Revision 1.204  2015/10/01 16:20:26  brouard
+   Summary: Some new graphs of contribution to likelihood
+   Revision 1.203  2015/09/30 17:45:14  brouard
+   Summary: looking at better estimation of the hessian
+   Also a better criteria for convergence to the period prevalence And
+   therefore adding the number of years needed to converge. (The
+   prevalence in any alive state shold sum to one
+   Revision 1.202  2015/09/22 19:45:16  brouard
+   Summary: Adding some overall graph on contribution to likelihood. Might change
+   Revision 1.201  2015/09/15 17:34:58  brouard
+   Summary: 0.98r0
+   - Some new graphs like suvival functions
+   - Some bugs fixed like model=1+age+V2.
+   Revision 1.200  2015/09/09 16:53:55  brouard
+   Summary: Big bug thanks to Flavia
+   Even model=1+age+V2. did not work anymore
+   Revision 1.199  2015/09/07 14:09:23  brouard
+   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+   Revision 1.198  2015/09/03 07:14:39  brouard
+   Summary: 0.98q5 Flavia
+   Revision 1.197  2015/09/01 18:24:39  brouard
+   *** empty log message ***
+   Revision 1.196  2015/08/18 23:17:52  brouard
+   Summary: 0.98q5
+   Revision 1.195  2015/08/18 16:28:39  brouard
+   Summary: Adding a hack for testing purpose
+   After reading the title, ftol and model lines, if the comment line has
+   a q, starting with #q, the answer at the end of the run is quit. It
+   permits to run test files in batch with ctest. The former workaround was
+   $ echo q | imach foo.imach
+   Revision 1.194  2015/08/18 13:32:00  brouard
+   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+   Revision 1.193  2015/08/04 07:17:42  brouard
+   Summary: 0.98q4
+   Revision 1.192  2015/07/16 16:49:02  brouard
+   Summary: Fixing some outputs
+   Revision 1.191  2015/07/14 10:00:33  brouard
+   Summary: Some fixes
+   Revision 1.190  2015/05/05 08:51:13  brouard
+   Summary: Adding digits in output parameters (7 digits instead of 6)
+   Fix 1+age+.
+   Revision 1.189  2015/04/30 14:45:16  brouard
+   Summary: 0.98q2
+   Revision 1.188  2015/04/30 08:27:53  brouard
+   *** empty log message ***
+   Revision 1.187  2015/04/29 09:11:15  brouard
+   *** empty log message ***
+   Revision 1.186  2015/04/23 12:01:52  brouard
+   Summary: V1*age is working now, version 0.98q1
+   Some codes had been disabled in order to simplify and Vn*age was
+   working in the optimization phase, ie, giving correct MLE parameters,
+   but, as usual, outputs were not correct and program core dumped.
+   Revision 1.185  2015/03/11 13:26:42  brouard
+   Summary: Inclusion of compile and links command line for Intel Compiler
+   Revision 1.184  2015/03/11 11:52:39  brouard
+   Summary: Back from Windows 8. Intel Compiler
+   Revision 1.183  2015/03/10 20:34:32  brouard
+   Summary: 0.98q0, trying with directest, mnbrak fixed
+   We use directest instead of original Powell test; probably no
+   incidence on the results, but better justifications;
+   We fixed Numerical Recipes mnbrak routine which was wrong and gave
+   wrong results.
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
+   Revision 1.168  2014/12/22 15:17:42  brouard
+   Summary: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
    Revision 1.125  2006/04/04 15:20:31  lievre
    Errors in calculation of health expectancies. Age was not initialized.
    Forecasting file added.
    Revision 1.124  2006/03/22 17:13:53  lievre
    Parameters are printed with %lf instead of %f (more numbers after the comma).
    The log-likelihood is printed in the log file
    Revision 1.123  2006/03/20 10:52:43  brouard
    * imach.c (Module): <title> changed, corresponds to .htm file
    name. <head> headers where missing.
    * imach.c (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.122  2006/03/20 09:45:41  brouard
    (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.121  2006/03/16 17:45:01  lievre
    * imach.c (Module): Comments concerning covariates added
    * imach.c (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.120  2006/03/16 15:10:38  lievre
    (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.119  2006/03/15 17:42:26  brouard
    (Module): Bug if status = -2, the loglikelihood was
    computed as likelihood omitting the logarithm. Version O.98e
    Revision 1.118  2006/03/14 18:20:07  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.117  2006/03/14 17:16:22  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.116  2006/03/06 10:29:27  brouard
    (Module): Variance-covariance wrong links and
    varian-covariance of ej. is needed (Saito).
    Revision 1.115  2006/02/27 12:17:45  brouard
    (Module): One freematrix added in mlikeli! 0.98c
    Revision 1.114  2006/02/26 12:57:58  brouard
    (Module): Some improvements in processing parameter
    filename with strsep.
    Revision 1.113  2006/02/24 14:20:24  brouard
    (Module): Memory leaks checks with valgrind and:
    datafile was not closed, some imatrix were not freed and on matrix
    allocation too.
    Revision 1.112  2006/01/30 09:55:26  brouard
    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    Revision 1.111  2006/01/25 20:38:18  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    (Module): Comments can be added in data file. Missing date values
    can be a simple dot '.'.
    Revision 1.110  2006/01/25 00:51:50  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    Revision 1.109  2006/01/24 19:37:15  brouard
    (Module): Comments (lines starting with a #) are allowed in data.
    Revision 1.108  2006/01/19 18:05:42  lievre
    Gnuplot problem appeared...
    To be fixed
    Revision 1.107  2006/01/19 16:20:37  brouard
    Test existence of gnuplot in imach path
    Revision 1.106  2006/01/19 13:24:36  brouard
    Some cleaning and links added in html output
    Revision 1.105  2006/01/05 20:23:19  lievre
    *** empty log message ***
    Revision 1.104  2005/09/30 16:11:43  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    (Module): If the status is missing at the last wave but we know
    that the person is alive, then we can code his/her status as -2
    (instead of missing=-1 in earlier versions) and his/her
    contributions to the likelihood is 1 - Prob of dying from last
    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    the healthy state at last known wave). Version is 0.98
    Revision 1.103  2005/09/30 15:54:49  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    Revision 1.102  2004/09/15 17:31:30  brouard
    Add the possibility to read data file including tab characters.
    Revision 1.101  2004/09/15 10:38:38  brouard
    Fix on curr_time
    Revision 1.100  2004/07/12 18:29:06  brouard
    Add version for Mac OS X. Just define UNIX in Makefile
    Revision 1.99  2004/06/05 08:57:40  brouard
    *** empty log message ***
    Revision 1.98  2004/05/16 15:05:56  brouard
    New version 0.97 . First attempt to estimate force of mortality
    directly from the data i.e. without the need of knowing the health
    state at each age, but using a Gompertz model: log u =a + b*age .
    This is the basic analysis of mortality and should be done before any
    other analysis, in order to test if the mortality estimated from the
    cross-longitudinal survey is different from the mortality estimated
    from other sources like vital statistic data.
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
    the slope with 95% confident intervals.
    Current limitations:
    A) Even if you enter covariates, i.e. with the
    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    B) There is no computation of Life Expectancy nor Life Table.
    Revision 1.97  2004/02/20 13:25:42  lievre
    Version 0.96d. Population forecasting command line is (temporarily)
    suppressed.
    Revision 1.96  2003/07/15 15:38:55  brouard
    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs.
    Revision 1.95  2003/07/08 07:54:34  brouard
    * imach.c (Repository):
    (Repository): Using imachwizard code to output a more meaningful covariance
    matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
    Revision 1.93  2003/06/25 16:33:55  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    (Module): Version 0.96b
    Revision 1.92  2003/06/25 16:30:45  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    Revision 1.91  2003/06/25 15:30:29  brouard
    * imach.c (Repository): Duplicated warning errors corrected.
    (Repository): Elapsed time after each iteration is now output. It
    helps to forecast when convergence will be reached. Elapsed time
    is stamped in powell.  We created a new html file for the graphs
    concerning matrix of covariance. It has extension -cov.htm.
    Revision 1.90  2003/06/24 12:34:15  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.88  2003/06/23 17:54:56  brouard
    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    Revision 1.87  2003/06/18 12:26:01  brouard
    Version 0.96
    Revision 1.86  2003/06/17 20:04:08  brouard
    (Module): Change position of html and gnuplot routines and added
    routine fileappend.
    Revision 1.85  2003/06/17 13:12:43  brouard
    * imach.c (Repository): Check when date of death was earlier that
    current date of interview. It may happen when the death was just
    prior to the death. In this case, dh was negative and likelihood
    was wrong (infinity). We still send an "Error" but patch by
    assuming that the date of death was just one stepm after the
    interview.
    (Repository): Because some people have very long ID (first column)
    we changed int to long in num[] and we added a new lvector for
    memory allocation. But we also truncated to 8 characters (left
    truncation)
    (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
    Revision 1.82  2003/06/05 15:57:20  brouard
    Add log in  imach.c and  fullversion number is now printed.
  */
  /*
     Interpolated Markov Chain
    Short summary of the programme:
    This program computes Healthy Life Expectancies from
    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    first survey ("cross") where individuals from different ages are
    interviewed on their health status or degree of disability (in the
    case of a health survey which is our main interest) -2- at least a
    second wave of interviews ("longitudinal") which measure each change
    (if any) in individual health status.  Health expectancies are
    computed from the time spent in each health state according to a
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
    probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
    complex model than "constant and age", you should modify the program
    where the markup *Covariates have to be included here again* invites
    you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
    multinomial logistic model, is clear when the delay between waves is not
    identical for each individual. Also, if a individual missed an
    intermediate interview, the information is lost, but taken into
    account using an interpolation or extrapolation.
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
    states. This elementary transition (by month, quarter,
    semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
  /*
    main
    read parameterfile
    read datafile
    concatwav
    freqsummary
    if (mle >= 1)
      mlikeli
    print results files
    if mle==1
       computes hessian
    read end of parameter file: agemin, agemax, bage, fage, estepm
        begin-prev-date,...
    open gnuplot file
    open html file
-   period (stable) prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
-   forecasting if prevfcast==1 prevforecast call prevalence()
-   health expectancies
+   h Pij x                         | pij_nom  ficrestpij
-   Variance-covariance of DFLE
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
-   prevalence()
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
-    movingaverage()
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
-   varevsij()
-   if popbased==1 varevsij(,popbased)
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
-   total life expectancies
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
-   Variance of period (stable) prevalence
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
-  end
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- */
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
- #include <math.h>
+   prevalence()
- #include <stdio.h>
+    movingaverage()
- #include <stdlib.h>
+   varevsij()
- #include <string.h>
+   if popbased==1 varevsij(,popbased)
- #include <unistd.h>
+   total life expectancies
+   Variance of period (stable) prevalence
- #include <limits.h>
+  end
- #include <sys/types.h>
+ */
- #include <sys/stat.h>
- #include <errno.h>
+ /* #define DEBUG */
- extern int errno;
+ /* #define DEBUGBRENT */
+ /* #define DEBUGLINMIN */
- /* #include <sys/time.h> */
+ /* #define DEBUGHESS */
- #include <time.h>
+ #define DEBUGHESSIJ
- #include "timeval.h"
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
+ #define POWELL /* Instead of NLOPT */
- /* #include <libintl.h> */
+ #define POWELLF1F3 /* Skip test */
- /* #define _(String) gettext (String) */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
- #define MAXLINE 256
+ #include <math.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <stdio.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <stdlib.h>
- #define FILENAMELENGTH 132
+ #include <string.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #ifdef _WIN32
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <io.h>
+ #include <windows.h>
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #include <tchar.h>
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #else
+ #include <unistd.h>
- #define NINTERVMAX 8
+ #endif
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #include <limits.h>
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #include <sys/types.h>
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #if defined(__GNUC__)
- #define AGESUP 130
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- #define AGEBASE 40
+ #endif
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #ifdef UNIX
+ #include <sys/stat.h>
- #define DIRSEPARATOR '/'
+ #include <errno.h>
- #define CHARSEPARATOR "/"
+ /* extern int errno; */
- #define ODIRSEPARATOR '\\'
- #else
+ /* #ifdef LINUX */
- #define DIRSEPARATOR '\\'
+ /* #include <time.h> */
- #define CHARSEPARATOR "\\"
+ /* #include "timeval.h" */
- #define ODIRSEPARATOR '/'
+ /* #else */
- #endif
+ /* #include <sys/time.h> */
+ /* #endif */
- /* $Id$ */
- /* $State$ */
+ #include <time.h>
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #ifdef GSL
- char fullversion[]="$Revision$ $Date$";
+ #include <gsl/gsl_errno.h>
- char strstart[80];
+ #include <gsl/gsl_multimin.h>
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #endif
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #ifdef NLOPT
- int npar=NPARMAX;
+ #include <nlopt.h>
- int nlstate=2; /* Number of live states */
+ typedef struct {
- int ndeath=1; /* Number of dead states */
+   double (* function)(double [] );
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ } myfunc_data ;
- int popbased=0;
+ #endif
- int *wav; /* Number of waves for this individuual 0 is possible */
+ /* #include <libintl.h> */
- int maxwav; /* Maxim number of waves */
+ /* #define _(String) gettext (String) */
- int jmin, jmax; /* min, max spacing between 2 waves */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define GNUPLOTPROGRAM "gnuplot"
- int mle, weightopt;
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define FILENAMELENGTH 132
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- double jmean; /* Mean space between 2 waves */
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficlog, *ficrespow;
+ #define NINTERVMAX 8
- int globpr; /* Global variable for printing or not */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- double fretone; /* Only one call to likelihood */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- long ipmx; /* Number of contributions */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- double sw; /* Sum of weights */
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
- char filerespow[FILENAMELENGTH];
+ #define MAXN 20000
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #define YEARM 12. /**< Number of months per year */
- FILE *ficresilk;
+ #define AGESUP 130
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define AGEBASE 40
- FILE *ficresprobmorprev;
+ #define AGEOVERFLOW 1.e20
- FILE *fichtm, *fichtmcov; /* Html File */
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- FILE *ficreseij;
+ #ifdef _WIN32
- char filerese[FILENAMELENGTH];
+ #define DIRSEPARATOR '\\'
- FILE *ficresstdeij;
+ #define CHARSEPARATOR "\\"
- char fileresstde[FILENAMELENGTH];
+ #define ODIRSEPARATOR '/'
- FILE *ficrescveij;
+ #else
- char filerescve[FILENAMELENGTH];
+ #define DIRSEPARATOR '/'
- FILE  *ficresvij;
+ #define CHARSEPARATOR "/"
- char fileresv[FILENAMELENGTH];
+ #define ODIRSEPARATOR '\\'
- FILE  *ficresvpl;
+ #endif
- char fileresvpl[FILENAMELENGTH];
- char title[MAXLINE];
+ /* $Id$ */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ /* $State$ */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ #include "version.h"
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char version[]=__IMACH_VERSION__;
- char command[FILENAMELENGTH];
+ char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- int  outcmd=0;
+ char fullversion[]="$Revision$ $Date$";
+ char strstart[80];
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- char filerest[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- char fileregp[FILENAMELENGTH];
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char popfile[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- struct timezone tzp;
+ int cptcov=0; /* Working variable */
- extern int gettimeofday();
+ int npar=NPARMAX;
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int nlstate=2; /* Number of live states */
- long time_value;
+ int ndeath=1; /* Number of dead states */
- extern long time();
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char strcurr[80], strfor[80];
+ int popbased=0;
- char *endptr;
+ int *wav; /* Number of waves for this individuual 0 is possible */
- long lval;
+ int maxwav=0; /* Maxim number of waves */
- double dval;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- #define NR_END 1
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- #define FREE_ARG char*
+                    to the likelihood and the sum of weights (done by funcone)*/
- #define FTOL 1.0e-10
+ int mle=1, weightopt=0;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- #define NRANSI
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- #define ITMAX 200
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- #define TOL 2.0e-4
+ int countcallfunc=0;  /* Count the number of calls to func */
+ double jmean=1; /* Mean space between 2 waves */
- #define CGOLD 0.3819660
+ double **matprod2(); /* test */
- #define ZEPS 1.0e-10
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ /*FILE *fic ; */ /* Used in readdata only */
- #define GOLD 1.618034
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- #define GLIMIT 100.0
+ FILE *ficlog, *ficrespow;
- #define TINY 1.0e-20
+ int globpr=0; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
- static double maxarg1,maxarg2;
+ long ipmx=0; /* Number of contributions */
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ double sw; /* Sum of weights */
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char filerespow[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ FILE *ficresilk;
- #define rint(a) floor(a+0.5)
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficresprobmorprev;
- static double sqrarg;
+ FILE *fichtm, *fichtmcov; /* Html File */
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ FILE *ficreseij;
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char filerese[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
- int imx;
+ FILE *ficrescveij;
- int stepm=1;
+ char filerescve[FILENAMELENGTH];
- /* Stepm, step in month: minimum step interpolation*/
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- int estepm;
+ FILE  *ficresvpl;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
- int m,nb;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- long *num;
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ char command[FILENAMELENGTH];
- double **pmmij, ***probs;
+ int  outcmd=0;
- double *ageexmed,*agecens;
- double dateintmean=0;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
- double *weight;
+ char filelog[FILENAMELENGTH]; /* Log file */
- int **s; /* Status */
+ char filerest[FILENAMELENGTH];
- double *agedc, **covar, idx;
+ char fileregp[FILENAMELENGTH];
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ char popfile[FILENAMELENGTH];
- double *lsurv, *lpop, *tpop;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
+ /* struct timezone tzp; */
- /**************** split *************************/
+ /* extern int gettimeofday(); */
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ struct tm tml, *gmtime(), *localtime();
- {
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ extern time_t time();
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
-   char  *ss;                            /* pointer */
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
-   int   l1, l2;                         /* length counters */
+ struct tm tm;
-   l1 = strlen(path );                   /* length of path */
+ char strcurr[80], strfor[80];
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ char *endptr;
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ long lval;
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ double dval;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define NR_END 1
-     /* get current working directory */
+ #define FREE_ARG char*
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define FTOL 1.0e-10
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-       return( GLOCK_ERROR_GETCWD );
+ #define NRANSI
-     }
+ #define ITMAX 200
-     /* got dirc from getcwd*/
-     printf(" DIRC = %s \n",dirc);
+ #define TOL 2.0e-4
-   } else {                              /* strip direcotry from path */
-     ss++;                               /* after this, the filename */
+ #define CGOLD 0.3819660
-     l2 = strlen( ss );                  /* length of filename */
+ #define ZEPS 1.0e-10
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     strcpy( name, ss );         /* save file name */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ #define GOLD 1.618034
-     dirc[l1-l2] = 0;                    /* add zero */
+ #define GLIMIT 100.0
-     printf(" DIRC2 = %s \n",dirc);
+ #define TINY 1.0e-20
-   }
-   /* We add a separator at the end of dirc if not exists */
+ static double maxarg1,maxarg2;
-   l1 = strlen( dirc );                  /* length of directory */
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     dirc[l1] =  DIRSEPARATOR;
-     dirc[l1+1] = 0;
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     printf(" DIRC3 = %s \n",dirc);
+ #define rint(a) floor(a+0.5)
-   }
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-   ss = strrchr( name, '.' );            /* find last / */
+ #define mytinydouble 1.0e-16
-   if (ss >0){
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     ss++;
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-     strcpy(ext,ss);                     /* save extension */
+ /* static double dsqrarg; */
-     l1= strlen( name);
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-     l2= strlen(ss)+1;
+ static double sqrarg;
-     strncpy( finame, name, l1-l2);
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-     finame[l1-l2]= 0;
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   }
+ int agegomp= AGEGOMP;
-   return( 0 );                          /* we're done */
+ int imx;
- }
+ int stepm=1;
+ /* Stepm, step in month: minimum step interpolation*/
- /******************************************/
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- void replace_back_to_slash(char *s, char*t)
- {
+ int m,nb;
-   int i;
+ long *num;
-   int lg=0;
+ int firstpass=0, lastpass=4,*cod, *cens;
-   i=0;
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
-   lg=strlen(t);
+                    covariate for which somebody answered excluding
-   for(i=0; i<= lg; i++) {
+                    undefined. Usually 2: 0 and 1. */
-     (s[i] = t[i]);
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
-     if (t[i]== '\\') s[i]='/';
+                              covariate for which somebody answered including
-   }
+                              undefined. Usually 3: -1, 0 and 1. */
- }
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ double **pmmij, ***probs;
- int nbocc(char *s, char occ)
+ double *ageexmed,*agecens;
- {
+ double dateintmean=0;
-   int i,j=0;
-   int lg=20;
+ double *weight;
-   i=0;
+ int **s; /* Status */
-   lg=strlen(s);
+ double *agedc;
-   for(i=0; i<= lg; i++) {
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   if  (s[i] == occ ) j++;
+                   * covar=matrix(0,NCOVMAX,1,n);
-   }
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
-   return j;
+ double  idx;
- }
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ int *Tage;
- void cutv(char *u,char *v, char*t, char occ)
+ int *Ndum; /** Freq of modality (tricode */
- {
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ double *lsurv, *lpop, *tpop;
-      gives u="abcedf" and v="ghi2j" */
-   int i,lg,j,p=0;
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-   i=0;
+ double ftolhess; /**< Tolerance for computing hessian */
-   for(j=0; j<=strlen(t)-1; j++) {
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ /**************** split *************************/
-   }
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ {
-   lg=strlen(t);
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   for(j=0; j<p; j++) {
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-     (u[j] = t[j]);
+   */
-   }
+   char  *ss;                            /* pointer */
-      u[p]='\0';
+   int   l1=0, l2=0;                             /* length counters */
-    for(j=0; j<= lg; j++) {
+   l1 = strlen(path );                   /* length of path */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   }
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- }
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
- /********************** nrerror ********************/
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- void nrerror(char error_text[])
+     /* get current working directory */
- {
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   fprintf(stderr,"ERREUR ...\n");
+ #ifdef WIN32
-   fprintf(stderr,"%s\n",error_text);
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   exit(EXIT_FAILURE);
+ #else
- }
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
- /*********************** vector *******************/
+ #endif
- double *vector(int nl, int nh)
+       return( GLOCK_ERROR_GETCWD );
- {
+     }
-   double *v;
+     /* got dirc from getcwd*/
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     printf(" DIRC = %s \n",dirc);
-   if (!v) nrerror("allocation failure in vector");
+   } else {                              /* strip directory from path */
-   return v-nl+NR_END;
+     ss++;                               /* after this, the filename */
- }
+     l2 = strlen( ss );                  /* length of filename */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
- /************************ free vector ******************/
+     strcpy( name, ss );         /* save file name */
- void free_vector(double*v, int nl, int nh)
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
- {
+     dirc[l1-l2] = '\0';                 /* add zero */
-   free((FREE_ARG)(v+nl-NR_END));
+     printf(" DIRC2 = %s \n",dirc);
- }
+   }
+   /* We add a separator at the end of dirc if not exists */
- /************************ivector *******************************/
+   l1 = strlen( dirc );                  /* length of directory */
- int *ivector(long nl,long nh)
+   if( dirc[l1-1] != DIRSEPARATOR ){
- {
+     dirc[l1] =  DIRSEPARATOR;
-   int *v;
+     dirc[l1+1] = 0;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+     printf(" DIRC3 = %s \n",dirc);
-   if (!v) nrerror("allocation failure in ivector");
+   }
-   return v-nl+NR_END;
+   ss = strrchr( name, '.' );            /* find last / */
- }
+   if (ss >0){
+     ss++;
- /******************free ivector **************************/
+     strcpy(ext,ss);                     /* save extension */
- void free_ivector(int *v, long nl, long nh)
+     l1= strlen( name);
- {
+     l2= strlen(ss)+1;
-   free((FREE_ARG)(v+nl-NR_END));
+     strncpy( finame, name, l1-l2);
- }
+     finame[l1-l2]= 0;
+   }
- /************************lvector *******************************/
- long *lvector(long nl,long nh)
+   return( 0 );                          /* we're done */
- {
+ }
-   long *v;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   if (!v) nrerror("allocation failure in ivector");
+ /******************************************/
-   return v-nl+NR_END;
- }
+ void replace_back_to_slash(char *s, char*t)
+ {
- /******************free lvector **************************/
+   int i;
- void free_lvector(long *v, long nl, long nh)
+   int lg=0;
- {
+   i=0;
-   free((FREE_ARG)(v+nl-NR_END));
+   lg=strlen(t);
- }
+   for(i=0; i<= lg; i++) {
+     (s[i] = t[i]);
- /******************* imatrix *******************************/
+     if (t[i]== '\\') s[i]='/';
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   }
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ }
- {
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ char *trimbb(char *out, char *in)
-   int **m;
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
-   /* allocate pointers to rows */
+   s=out;
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   while (*in != '\0'){
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-   m += NR_END;
+       in++;
-   m -= nrl;
+     }
+     *out++ = *in++;
+   }
-   /* allocate rows and set pointers to them */
+   *out='\0';
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   return s;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ }
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+ /* char *substrchaine(char *out, char *in, char *chain) */
+ /* { */
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+ /*   char *s, *t; */
-   /* return pointer to array of pointers to rows */
+ /*   t=in;s=out; */
-   return m;
+ /*   while ((*in != *chain) && (*in != '\0')){ */
- }
+ /*     *out++ = *in++; */
+ /*   } */
- /****************** free_imatrix *************************/
- void free_imatrix(m,nrl,nrh,ncl,nch)
+ /*   /\* *in matches *chain *\/ */
-       int **m;
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
-       long nch,ncl,nrh,nrl;
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
-      /* free an int matrix allocated by imatrix() */
+ /*   } */
- {
+ /*   in--; chain--; */
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ /*   while ( (*in != '\0')){ */
-   free((FREE_ARG) (m+nrl-NR_END));
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- }
+ /*     *out++ = *in++; */
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
- /******************* matrix *******************************/
+ /*   } */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+ /*   *out='\0'; */
- {
+ /*   out=s; */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ /*   return out; */
-   double **m;
+ /* } */
+ char *substrchaine(char *out, char *in, char *chain)
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ {
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   /* Substract chain 'chain' from 'in', return and output 'out' */
-   m += NR_END;
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
-   m -= nrl;
+   char *strloc;
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   strcpy (out, in);
-   m[nrl] += NR_END;
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
-   m[nrl] -= ncl;
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+   if(strloc != NULL){
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
-   return m;
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+     /* strcpy (strloc, strloc +strlen(chain));*/
-    */
+   }
- }
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   return out;
- /*************************free matrix ************************/
+ }
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
- {
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-   free((FREE_ARG)(m+nrl-NR_END));
+ {
- }
+   /* 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')
- /******************* ma3x *******************************/
+      gives blocc="abcdef" and alocc="ghi2j".
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- {
+   */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   char *s, *t;
-   double ***m;
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+     *alocc++ = *in++;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   }
-   m += NR_END;
+   if( *in == occ){
-   m -= nrl;
+     *(alocc)='\0';
+     s=++in;
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+   if (s == t) {/* occ not found */
-   m[nrl] -= ncl;
+     *(alocc-(in-s))='\0';
+     in=s;
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   }
+   while ( *in != '\0'){
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+     *blocc++ = *in++;
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   }
-   m[nrl][ncl] += NR_END;
-   m[nrl][ncl] -= nll;
+   *blocc='\0';
-   for (j=ncl+1; j<=nch; j++)
+   return t;
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   for (i=nrl+1; i<=nrh; i++) {
+ {
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
-     for (j=ncl+1; j<=nch; j++)
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-       m[i][j]=m[i][j-1]+nlay;
+      gives blocc="abcdef2ghi" and alocc="j".
-   }
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   return m;
+   */
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   char *s, *t;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   t=in;s=in;
-   */
+   while (*in != '\0'){
- }
+     while( *in == occ){
+       *blocc++ = *in++;
- /*************************free ma3x ************************/
+       s=in;
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+     }
- {
+     *blocc++ = *in++;
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   }
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   if (s == t) /* occ not found */
-   free((FREE_ARG)(m+nrl-NR_END));
+     *(blocc-(in-s))='\0';
- }
+   else
+     *(blocc-(in-s)-1)='\0';
- /*************** function subdirf ***********/
+   in=s;
- char *subdirf(char fileres[])
+   while ( *in != '\0'){
- {
+     *alocc++ = *in++;
-   /* Caution optionfilefiname is hidden */
+   }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/"); /* Add to the right */
+   *alocc='\0';
-   strcat(tmpout,fileres);
+   return s;
-   return tmpout;
+ }
- }
+ int nbocc(char *s, char occ)
- /*************** function subdirf2 ***********/
+ {
- char *subdirf2(char fileres[], char *preop)
+   int i,j=0;
- {
+   int lg=20;
+   i=0;
-   /* Caution optionfilefiname is hidden */
+   lg=strlen(s);
-   strcpy(tmpout,optionfilefiname);
+   for(i=0; i<= lg; i++) {
-   strcat(tmpout,"/");
+   if  (s[i] == occ ) j++;
-   strcat(tmpout,preop);
+   }
-   strcat(tmpout,fileres);
+   return j;
-   return tmpout;
+ }
- }
+ /* void cutv(char *u,char *v, char*t, char occ) */
- /*************** function subdirf3 ***********/
+ /* { */
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- {
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   /* Caution optionfilefiname is hidden */
+ /*   int i,lg,j,p=0; */
-   strcpy(tmpout,optionfilefiname);
+ /*   i=0; */
-   strcat(tmpout,"/");
+ /*   lg=strlen(t); */
-   strcat(tmpout,preop);
+ /*   for(j=0; j<=lg-1; j++) { */
-   strcat(tmpout,preop2);
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   strcat(tmpout,fileres);
+ /*   } */
-   return tmpout;
- }
+ /*   for(j=0; j<p; j++) { */
+ /*     (u[j] = t[j]); */
- /***************** f1dim *************************/
+ /*   } */
- extern int ncom;
+ /*      u[p]='\0'; */
- extern double *pcom,*xicom;
- extern double (*nrfunc)(double []);
+ /*    for(j=0; j<= lg; j++) { */
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
- double f1dim(double x)
+ /*   } */
- {
+ /* } */
-   int j;
-   double f;
+ #ifdef _WIN32
-   double *xt;
+ char * strsep(char **pp, const char *delim)
+ {
-   xt=vector(1,ncom);
+   char *p, *q;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   f=(*nrfunc)(xt);
+   if ((p = *pp) == NULL)
-   free_vector(xt,1,ncom);
+     return 0;
-   return f;
+   if ((q = strpbrk (p, delim)) != NULL)
- }
+   {
+     *pp = q + 1;
- /*****************brent *************************/
+     *q = '\0';
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   }
- {
+   else
-   int iter;
+     *pp = 0;
-   double a,b,d,etemp;
+   return p;
-   double fu,fv,fw,fx;
+ }
-   double ftemp;
+ #endif
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   double e=0.0;
+ /********************** nrerror ********************/
-   a=(ax < cx ? ax : cx);
+ void nrerror(char error_text[])
-   b=(ax > cx ? ax : cx);
+ {
-   x=w=v=bx;
+   fprintf(stderr,"ERREUR ...\n");
-   fw=fv=fx=(*f)(x);
+   fprintf(stderr,"%s\n",error_text);
-   for (iter=1;iter<=ITMAX;iter++) {
+   exit(EXIT_FAILURE);
-     xm=0.5*(a+b);
+ }
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ /*********************** vector *******************/
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ double *vector(int nl, int nh)
-     printf(".");fflush(stdout);
+ {
-     fprintf(ficlog,".");fflush(ficlog);
+   double *v;
- #ifdef DEBUG
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-     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);
+   if (!v) nrerror("allocation failure in vector");
-     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);
+   return v-nl+NR_END;
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+ }
- #endif
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ /************************ free vector ******************/
-       *xmin=x;
+ void free_vector(double*v, int nl, int nh)
-       return fx;
+ {
-     }
+   free((FREE_ARG)(v+nl-NR_END));
-     ftemp=fu;
+ }
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+ /************************ivector *******************************/
-       q=(x-v)*(fx-fw);
+ int *ivector(long nl,long nh)
-       p=(x-v)*q-(x-w)*r;
+ {
-       q=2.0*(q-r);
+   int *v;
-       if (q > 0.0) p = -p;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-       q=fabs(q);
+   if (!v) nrerror("allocation failure in ivector");
-       etemp=e;
+   return v-nl+NR_END;
-       e=d;
+ }
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /******************free ivector **************************/
-       else {
+ void free_ivector(int *v, long nl, long nh)
-         d=p/q;
+ {
-         u=x+d;
+   free((FREE_ARG)(v+nl-NR_END));
-         if (u-a < tol2 || b-u < tol2)
+ }
-           d=SIGN(tol1,xm-x);
-       }
+ /************************lvector *******************************/
-     } else {
+ long *lvector(long nl,long nh)
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ {
-     }
+   long *v;
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-     fu=(*f)(u);
+   if (!v) nrerror("allocation failure in ivector");
-     if (fu <= fx) {
+   return v-nl+NR_END;
-       if (u >= x) a=x; else b=x;
+ }
-       SHFT(v,w,x,u)
-         SHFT(fv,fw,fx,fu)
+ /******************free lvector **************************/
-         } else {
+ void free_lvector(long *v, long nl, long nh)
-           if (u < x) a=u; else b=u;
+ {
-           if (fu <= fw || w == x) {
+   free((FREE_ARG)(v+nl-NR_END));
-             v=w;
+ }
-             w=u;
-             fv=fw;
+ /******************* imatrix *******************************/
-             fw=fu;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-           } else if (fu <= fv || v == x || v == w) {
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-             v=u;
+ {
-             fv=fu;
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-           }
+   int **m;
-         }
-   }
+   /* allocate pointers to rows */
-   nrerror("Too many iterations in brent");
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   *xmin=x;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   return fx;
+   m += NR_END;
- }
+   m -= nrl;
- /****************** mnbrak ***********************/
+   /* allocate rows and set pointers to them */
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-             double (*func)(double))
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- {
+   m[nrl] += NR_END;
-   double ulim,u,r,q, dum;
+   m[nrl] -= ncl;
-   double fu;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   *fa=(*func)(*ax);
-   *fb=(*func)(*bx);
+   /* return pointer to array of pointers to rows */
-   if (*fb > *fa) {
+   return m;
-     SHFT(dum,*ax,*bx,dum)
+ }
-       SHFT(dum,*fb,*fa,dum)
-       }
+ /****************** free_imatrix *************************/
-   *cx=(*bx)+GOLD*(*bx-*ax);
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   *fc=(*func)(*cx);
+       int **m;
-   while (*fb > *fc) {
+       long nch,ncl,nrh,nrl;
-     r=(*bx-*ax)*(*fb-*fc);
+      /* free an int matrix allocated by imatrix() */
-     q=(*bx-*cx)*(*fb-*fa);
+ {
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   free((FREE_ARG) (m+nrl-NR_END));
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+ }
-     if ((*bx-u)*(u-*cx) > 0.0) {
-       fu=(*func)(u);
+ /******************* matrix *******************************/
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       fu=(*func)(u);
+ {
-       if (fu < *fc) {
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   double **m;
-           SHFT(*fb,*fc,fu,(*func)(u))
-           }
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       u=ulim;
+   m += NR_END;
-       fu=(*func)(u);
+   m -= nrl;
-     } else {
-       u=(*cx)+GOLD*(*cx-*bx);
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       fu=(*func)(u);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-     }
+   m[nrl] += NR_END;
-     SHFT(*ax,*bx,*cx,u)
+   m[nrl] -= ncl;
-       SHFT(*fa,*fb,*fc,fu)
-       }
+   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]) or &(m[1][0])
- /*************** linmin ************************/
+ 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.
- int ncom;
+    */
- double *pcom,*xicom;
+ }
- double (*nrfunc)(double []);
+ /*************************free matrix ************************/
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
  {
-   double brent(double ax, double bx, double cx,
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-                double (*f)(double), double tol, double *xmin);
+   free((FREE_ARG)(m+nrl-NR_END));
-   double f1dim(double x);
+ }
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-               double *fc, double (*func)(double));
+ /******************* ma3x *******************************/
-   int j;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-   double xx,xmin,bx,ax;
+ {
-   double fx,fb,fa;
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   double ***m;
-   ncom=n;
-   pcom=vector(1,n);
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   xicom=vector(1,n);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   nrfunc=func;
+   m += NR_END;
-   for (j=1;j<=n;j++) {
+   m -= nrl;
-     pcom[j]=p[j];
-     xicom[j]=xi[j];
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   }
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   ax=0.0;
+   m[nrl] += NR_END;
-   xx=1.0;
+   m[nrl] -= ncl;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
- #endif
+   m[nrl][ncl] += NR_END;
-   for (j=1;j<=n;j++) {
+   m[nrl][ncl] -= nll;
-     xi[j] *= xmin;
+   for (j=ncl+1; j<=nch; j++)
-     p[j] += xi[j];
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   }
-   free_vector(xicom,1,n);
+   for (i=nrl+1; i<=nrh; i++) {
-   free_vector(pcom,1,n);
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- }
+     for (j=ncl+1; j<=nch; j++)
+       m[i][j]=m[i][j-1]+nlay;
- char *asc_diff_time(long time_sec, char ascdiff[])
+   }
- {
+   return m;
-   long sec_left, days, hours, minutes;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   days = (time_sec) / (60*60*24);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   sec_left = (time_sec) % (60*60*24);
+   */
-   hours = (sec_left) / (60*60) ;
+ }
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
+ /*************************free ma3x ************************/
-   sec_left = (sec_left) % (60);
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ {
-   return ascdiff;
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
- }
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   free((FREE_ARG)(m+nrl-NR_END));
- /*************** powell ************************/
+ }
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-             double (*func)(double []))
+ /*************** function subdirf ***********/
- {
+ char *subdirf(char fileres[])
-   void linmin(double p[], double xi[], int n, double *fret,
+ {
-               double (*func)(double []));
+   /* Caution optionfilefiname is hidden */
-   int i,ibig,j;
+   strcpy(tmpout,optionfilefiname);
-   double del,t,*pt,*ptt,*xit;
+   strcat(tmpout,"/"); /* Add to the right */
-   double fp,fptt;
+   strcat(tmpout,fileres);
-   double *xits;
+   return tmpout;
-   int niterf, itmp;
+ }
-   pt=vector(1,n);
+ /*************** function subdirf2 ***********/
-   ptt=vector(1,n);
+ char *subdirf2(char fileres[], char *preop)
-   xit=vector(1,n);
+ {
-   xits=vector(1,n);
-   *fret=(*func)(p);
+   /* Caution optionfilefiname is hidden */
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   strcpy(tmpout,optionfilefiname);
-   for (*iter=1;;++(*iter)) {
+   strcat(tmpout,"/");
-     fp=(*fret);
+   strcat(tmpout,preop);
-     ibig=0;
+   strcat(tmpout,fileres);
-     del=0.0;
+   return tmpout;
-     last_time=curr_time;
+ }
-     (void) gettimeofday(&curr_time,&tzp);
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+ /*************** function subdirf3 ***********/
-     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);
+ char *subdirf3(char fileres[], char *preop, char *preop2)
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+ {
-    for (i=1;i<=n;i++) {
-       printf(" %d %.12f",i, p[i]);
+   /* Caution optionfilefiname is hidden */
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   strcpy(tmpout,optionfilefiname);
-       fprintf(ficrespow," %.12lf", p[i]);
+   strcat(tmpout,"/");
-     }
+   strcat(tmpout,preop);
-     printf("\n");
+   strcat(tmpout,preop2);
-     fprintf(ficlog,"\n");
+   strcat(tmpout,fileres);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   return tmpout;
-     if(*iter <=3){
+ }
-       tm = *localtime(&curr_time.tv_sec);
-       strcpy(strcurr,asctime(&tm));
+ char *asc_diff_time(long time_sec, char ascdiff[])
- /*       asctime_r(&tm,strcurr); */
+ {
-       forecast_time=curr_time;
+   long sec_left, days, hours, minutes;
-       itmp = strlen(strcurr);
+   days = (time_sec) / (60*60*24);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   sec_left = (time_sec) % (60*60*24);
-         strcurr[itmp-1]='\0';
+   hours = (sec_left) / (60*60) ;
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   sec_left = (sec_left) %(60*60);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   minutes = (sec_left) /60;
-       for(niterf=10;niterf<=30;niterf+=10){
+   sec_left = (sec_left) % (60);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-         tmf = *localtime(&forecast_time.tv_sec);
+   return ascdiff;
- /*      asctime_r(&tmf,strfor); */
+ }
-         strcpy(strfor,asctime(&tmf));
-         itmp = strlen(strfor);
+ /***************** f1dim *************************/
-         if(strfor[itmp-1]=='\n')
+ extern int ncom;
-         strfor[itmp-1]='\0';
+ extern double *pcom,*xicom;
-         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);
+ extern double (*nrfunc)(double []);
-         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);
-       }
+ double f1dim(double x)
-     }
+ {
-     for (i=1;i<=n;i++) {
+   int j;
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   double f;
-       fptt=(*fret);
+   double *xt;
- #ifdef DEBUG
-       printf("fret=%lf \n",*fret);
+   xt=vector(1,ncom);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
- #endif
+   f=(*nrfunc)(xt);
-       printf("%d",i);fflush(stdout);
+   free_vector(xt,1,ncom);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+   return f;
-       linmin(p,xit,n,fret,func);
+ }
-       if (fabs(fptt-(*fret)) > del) {
-         del=fabs(fptt-(*fret));
+ /*****************brent *************************/
-         ibig=i;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-       }
+ {
- #ifdef DEBUG
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
-       printf("%d %.12e",i,(*fret));
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
-       for (j=1;j<=n;j++) {
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+    * returned function value.
-         printf(" x(%d)=%.12e",j,xit[j]);
+   */
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   int iter;
-       }
+   double a,b,d,etemp;
-       for(j=1;j<=n;j++) {
+   double fu=0,fv,fw,fx;
-         printf(" p=%.12e",p[j]);
+   double ftemp=0.;
-         fprintf(ficlog," p=%.12e",p[j]);
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-       }
+   double e=0.0;
-       printf("\n");
-       fprintf(ficlog,"\n");
+   a=(ax < cx ? ax : cx);
- #endif
+   b=(ax > cx ? ax : cx);
-     }
+   x=w=v=bx;
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   fw=fv=fx=(*f)(x);
- #ifdef DEBUG
+   for (iter=1;iter<=ITMAX;iter++) {
-       int k[2],l;
+     xm=0.5*(a+b);
-       k[0]=1;
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-       k[1]=-1;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-       printf("Max: %.12e",(*func)(p));
+     printf(".");fflush(stdout);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+     fprintf(ficlog,".");fflush(ficlog);
-       for (j=1;j<=n;j++) {
+ #ifdef DEBUGBRENT
-         printf(" %.12e",p[j]);
+     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-         fprintf(ficlog," %.12e",p[j]);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-       }
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-       printf("\n");
+ #endif
-       fprintf(ficlog,"\n");
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       for(l=0;l<=1;l++) {
+       *xmin=x;
-         for (j=1;j<=n;j++) {
+       return fx;
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+     }
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+     ftemp=fu;
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+     if (fabs(e) > tol1) {
-         }
+       r=(x-w)*(fx-fv);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       q=(x-v)*(fx-fw);
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       p=(x-v)*q-(x-w)*r;
-       }
+       q=2.0*(q-r);
- #endif
+       if (q > 0.0) p = -p;
+       q=fabs(q);
+       etemp=e;
-       free_vector(xit,1,n);
+       e=d;
-       free_vector(xits,1,n);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-       free_vector(ptt,1,n);
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       free_vector(pt,1,n);
+       else {
-       return;
+         d=p/q;
-     }
+         u=x+d;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+         if (u-a < tol2 || b-u < tol2)
-     for (j=1;j<=n;j++) {
+           d=SIGN(tol1,xm-x);
-       ptt[j]=2.0*p[j]-pt[j];
+       }
-       xit[j]=p[j]-pt[j];
+     } else {
-       pt[j]=p[j];
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
      }
-     fptt=(*func)(ptt);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-     if (fptt < fp) {
+     fu=(*f)(u);
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+     if (fu <= fx) {
-       if (t < 0.0) {
+       if (u >= x) a=x; else b=x;
-         linmin(p,xit,n,fret,func);
+       SHFT(v,w,x,u)
-         for (j=1;j<=n;j++) {
+       SHFT(fv,fw,fx,fu)
-           xi[j][ibig]=xi[j][n];
+     } else {
-           xi[j][n]=xit[j];
+       if (u < x) a=u; else b=u;
-         }
+       if (fu <= fw || w == x) {
- #ifdef DEBUG
+         v=w;
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         w=u;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         fv=fw;
-         for(j=1;j<=n;j++){
+         fw=fu;
-           printf(" %.12e",xit[j]);
+       } else if (fu <= fv || v == x || v == w) {
-           fprintf(ficlog," %.12e",xit[j]);
+         v=u;
-         }
+         fv=fu;
-         printf("\n");
+       }
-         fprintf(ficlog,"\n");
+     }
- #endif
+   }
-       }
+   nrerror("Too many iterations in brent");
-     }
+   *xmin=x;
-   }
+   return fx;
  }
- /**** Prevalence limit (stable or period prevalence)  ****************/
+ /****************** mnbrak ***********************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
- {
+             double (*func)(double))
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
-      matrix by transitions matrix until convergence is reached */
+ 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
-   int i, ii,j,k;
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
-   double min, max, maxmin, maxmax,sumnew=0.;
+    */
-   double **matprod2();
+   double ulim,u,r,q, dum;
-   double **out, cov[NCOVMAX], **pmij();
+   double fu;
-   double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   double scale=10.;
+   int iterscale=0;
-   for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (j=1;j<=nlstate+ndeath;j++){
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
-     }
-    cov[1]=1.;
+   /* 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++); */
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
-     newm=savm;
+   /* } */
-     /* Covariates have to be included here again */
-      cov[2]=agefin;
+   if (*fb > *fa) {
+     SHFT(dum,*ax,*bx,dum)
-       for (k=1; k<=cptcovn;k++) {
+     SHFT(dum,*fb,*fa,dum)
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   }
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       }
+   *fc=(*func)(*cx);
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ #ifdef DEBUG
-       for (k=1; k<=cptcovprod;k++)
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+ #endif
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     r=(*bx-*ax)*(*fb-*fc);
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     q=(*bx-*cx)*(*fb-*fa);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     savm=oldm;
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-     oldm=newm;
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-     maxmax=0.;
+       fu=(*func)(u);
-     for(j=1;j<=nlstate;j++){
+ #ifdef DEBUG
-       min=1.;
+       /* f(x)=A(x-u)**2+f(u) */
-       max=0.;
+       double A, fparabu;
-       for(i=1; i<=nlstate; i++) {
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         sumnew=0;
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       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);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+       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);
-         max=FMAX(max,prlim[i][j]);
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-         min=FMIN(min,prlim[i][j]);
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-       }
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-       maxmin=max-min;
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-       maxmax=FMAX(maxmax,maxmin);
+ #endif
-     }
+ #ifdef MNBRAKORIGINAL
-     if(maxmax < ftolpl){
+ #else
-       return prlim;
+ /*       if (fu > *fc) { */
-     }
+ /* #ifdef DEBUG */
-   }
+ /*       printf("mnbrak4  fu > fc \n"); */
- }
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
+ /* #endif */
- /*************** transition probabilities ***************/
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ /*      dum=u; /\* Shifting c and u *\/ */
- {
+ /*      u = *cx; */
-   double s1, s2;
+ /*      *cx = dum; */
-   /*double t34;*/
+ /*      dum = fu; */
-   int i,j,j1, nc, ii, jj;
+ /*      fu = *fc; */
+ /*      *fc =dum; */
-     for(i=1; i<= nlstate; i++){
+ /*       } else { /\* end *\/ */
-       for(j=1; j<i;j++){
+ /* #ifdef DEBUG */
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ /*       printf("mnbrak3  fu < fc \n"); */
-           /*s2 += param[i][j][nc]*cov[nc];*/
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /* #endif */
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*      dum=u; /\* Shifting c and u *\/ */
-         }
+ /*      u = *cx; */
-         ps[i][j]=s2;
+ /*      *cx = dum; */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ /*      dum = fu; */
-       }
+ /*      fu = *fc; */
-       for(j=i+1; j<=nlstate+ndeath;j++){
+ /*      *fc =dum; */
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ /*       } */
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ #ifdef DEBUG
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+       printf("mnbrak34  fu < or >= fc \n");
-         }
+       fprintf(ficlog, "mnbrak34 fu < fc\n");
-         ps[i][j]=s2;
+ #endif
-       }
+       dum=u; /* Shifting c and u */
-     }
+       u = *cx;
-     /*ps[3][2]=1;*/
+       *cx = dum;
+       dum = fu;
-     for(i=1; i<= nlstate; i++){
+       fu = *fc;
-       s1=0;
+       *fc =dum;
-       for(j=1; j<i; j++)
+ #endif
-         s1+=exp(ps[i][j]);
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ #ifdef DEBUG
-         s1+=exp(ps[i][j]);
+       printf("mnbrak2  u after c but before ulim\n");
-       ps[i][i]=1./(s1+1.);
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
-       for(j=1; j<i; j++)
+ #endif
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       fu=(*func)(u);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       if (fu < *fc) {
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ #ifdef DEBUG
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
-     } /* end i */
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
+ #endif
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+         SHFT(*fb,*fc,fu,(*func)(u))
-         ps[ii][jj]=0;
+       }
-         ps[ii][ii]=1;
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-       }
+ #ifdef DEBUG
-     }
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
+ #endif
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       u=ulim;
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       fu=(*func)(u);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
- /*       } */
+ #ifdef DEBUG
- /*       printf("\n "); */
+       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");
- /*        printf("\n ");printf("%lf ",cov[2]); */
+ #endif
-        /*
+       u=(*cx)+GOLD*(*cx-*bx);
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       fu=(*func)(u);
-       goto end;*/
+     } /* end tests */
-     return ps;
+     SHFT(*ax,*bx,*cx,u)
- }
+     SHFT(*fa,*fb,*fc,fu)
+ #ifdef DEBUG
- /**************** Product of 2 matrices ******************/
+       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);
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ #endif
- {
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-   /* 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(...) */
-   /* in, b, out are matrice of pointers which should have been initialized
+ /*************** linmin ************************/
-      before: only the contents of out is modified. The function returns
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-      a pointer to pointers identical to out */
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-   long i, j, k;
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-   for(i=nrl; i<= nrh; i++)
+ the value of func at the returned location p . This is actually all accomplished by calling the
-     for(k=ncolol; k<=ncoloh; k++)
+ routines mnbrak and brent .*/
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+ int ncom;
-         out[i][k] +=in[i][j]*b[j][k];
+ double *pcom,*xicom;
+ double (*nrfunc)(double []);
-   return out;
- }
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ {
+   double brent(double ax, double bx, double cx,
- /************* Higher Matrix Product ***************/
+                double (*f)(double), double tol, double *xmin);
+   double f1dim(double x);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
- {
+               double *fc, double (*func)(double));
-   /* Computes the transition matrix starting at age 'age' over
+   int j;
-      'nhstepm*hstepm*stepm' months (i.e. until
+   double xx,xmin,bx,ax;
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+   double fx,fb,fa;
-      nhstepm*hstepm matrices.
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+ #ifdef LINMINORIGINAL
-      (typically every 2 years instead of every month which is too big
+ #else
-      for the memory).
+   double scale=10., axs, xxs; /* Scale added for infinity */
-      Model is determined by parameters x and covariates have to be
+ #endif
-      included manually here.
+   ncom=n;
-      */
+   pcom=vector(1,n);
+   xicom=vector(1,n);
-   int i, j, d, h, k;
+   nrfunc=func;
-   double **out, cov[NCOVMAX];
+   for (j=1;j<=n;j++) {
-   double **newm;
+     pcom[j]=p[j];
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
-   /* Hstepm could be zero and should return the unit matrix */
+   }
-   for (i=1;i<=nlstate+ndeath;i++)
-     for (j=1;j<=nlstate+ndeath;j++){
+ #ifdef LINMINORIGINAL
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+   xx=1.;
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+ #else
-     }
+   axs=0.0;
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   xxs=1.;
-   for(h=1; h <=nhstepm; h++){
+   do{
-     for(d=1; d <=hstepm; d++){
+     xx= xxs;
-       newm=savm;
+ #endif
-       /* Covariates have to be included here again */
+     ax=0.;
-       cov[1]=1.;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     /* 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 (k=1; k<=cptcovage;k++)
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
-       for (k=1; k<=cptcovprod;k++)
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     /* 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]]*/
+ #ifdef LINMINORIGINAL
+ #else
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+     if (fx != fx){
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+         printf("|");
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+         fprintf(ficlog,"|");
-       savm=oldm;
+ #ifdef DEBUGLINMIN
-       oldm=newm;
+         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
-     }
+ #endif
-     for(i=1; i<=nlstate+ndeath; i++)
+     }
-       for(j=1;j<=nlstate+ndeath;j++) {
+   }while(fx != fx);
-         po[i][j][h]=newm[i][j];
+ #endif
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
-          */
+ #ifdef DEBUGLINMIN
-       }
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
-   } /* end h */
+   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
-   return po;
+ #endif
- }
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
+   /* fmin = f(p[j] + xmin * xi[j]) */
- /*************** log-likelihood *************/
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
- double func( double *x)
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
- {
+ #ifdef DEBUG
-   int i, ii, j, k, mi, d, kk;
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   double **out;
+ #endif
-   double sw; /* Sum of weights */
+ #ifdef DEBUGLINMIN
-   double lli; /* Individual log likelihood */
+   printf("linmin end ");
-   int s1, s2;
+   fprintf(ficlog,"linmin end ");
-   double bbh, survp;
+ #endif
-   long ipmx;
+   for (j=1;j<=n;j++) {
-   /*extern weight */
+ #ifdef LINMINORIGINAL
-   /* We are differentiating ll according to initial status */
+     xi[j] *= xmin;
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ #else
-   /*for(i=1;i<imx;i++)
+ #ifdef DEBUGLINMIN
-     printf(" %d\n",s[4][i]);
+     if(xxs <1.0)
-   */
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
-   cov[1]=1.;
+ #endif
+     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
-   if(mle==1){
+       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 );
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #endif
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #endif
-       for(mi=1; mi<= wav[i]-1; mi++){
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   }
-           for (j=1;j<=nlstate+ndeath;j++){
+ #ifdef DEBUGLINMIN
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   printf("\n");
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-           }
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
-         for(d=0; d<dh[mi][i]; d++){
+   for (j=1;j<=n;j++) {
-           newm=savm;
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
-           for (kk=1; kk<=cptcovage;kk++) {
+     if(j % ncovmodel == 0){
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       printf("\n");
-           }
+       fprintf(ficlog,"\n");
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   }
-           savm=oldm;
+ #else
-           oldm=newm;
+ #endif
-         } /* end mult */
+   free_vector(xicom,1,n);
+   free_vector(pcom,1,n);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+ }
-         /* But now since version 0.9 we anticipate for bias at large stepm.
-          * 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
+ /*************** powell ************************/
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+ /*
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+ Minimization of a function func of n variables. Input consists of an initial starting point
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-          * probability in order to take into account the bias as a fraction of the way
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-          * -stepm/2 to stepm/2 .
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-          * For stepm=1 the results are the same as for previous versions of Imach.
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-          * For stepm > 1 the results are less biased than in previous versions.
+  */
-          */
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         s1=s[mw[mi][i]][i];
+             double (*func)(double []))
-         s2=s[mw[mi+1][i]][i];
+ {
-         bbh=(double)bh[mi][i]/(double)stepm;
+   void linmin(double p[], double xi[], int n, double *fret,
-         /* bias bh is positive if real duration
+               double (*func)(double []));
-          * is higher than the multiple of stepm and negative otherwise.
+   int i,ibig,j;
-          */
+   double del,t,*pt,*ptt,*xit;
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+   double directest;
-         if( s2 > nlstate){
+   double fp,fptt;
-           /* i.e. if s2 is a death state and if the date of death is known
+   double *xits;
-              then the contribution to the likelihood is the probability to
+   int niterf, itmp;
-              die between last step unit time and current  step unit time,
-              which is also equal to probability to die before dh
+   pt=vector(1,n);
-              minus probability to die before dh-stepm .
+   ptt=vector(1,n);
-              In version up to 0.92 likelihood was computed
+   xit=vector(1,n);
-         as if date of death was unknown. Death was treated as any other
+   xits=vector(1,n);
-         health state: the date of the interview describes the actual state
+   *fret=(*func)(p);
-         and not the date of a change in health state. The former idea was
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         to consider that at each interview the state was recorded
+   rcurr_time = time(NULL);
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   for (*iter=1;;++(*iter)) {
-         introduced the exact date of death then we should have modified
+     fp=(*fret); /* From former iteration or initial value */
-         the contribution of an exact death to the likelihood. This new
+     ibig=0;
-         contribution is smaller and very dependent of the step unit
+     del=0.0;
-         stepm. It is no more the probability to die between last interview
+     rlast_time=rcurr_time;
-         and month of death but the probability to survive from last
+     /* (void) gettimeofday(&curr_time,&tzp); */
-         interview up to one month before death multiplied by the
+     rcurr_time = time(NULL);
-         probability to die within a month. Thanks to Chris
+     curr_time = *localtime(&rcurr_time);
-         Jackson for correcting this bug.  Former versions increased
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-         mortality artificially. The bad side is that we add another loop
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-         which slows down the processing. The difference can be up to 10%
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-         lower mortality.
+     for (i=1;i<=n;i++) {
-           */
+       printf(" %d %.12f",i, p[i]);
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       fprintf(ficlog," %d %.12lf",i, p[i]);
+       fprintf(ficrespow," %.12lf", p[i]);
+     }
-         } else if  (s2==-2) {
+     printf("\n");
-           for (j=1,survp=0. ; j<=nlstate; j++)
+     fprintf(ficlog,"\n");
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-           /*survp += out[s1][j]; */
+     if(*iter <=3){
-           lli= log(survp);
+       tml = *localtime(&rcurr_time);
-         }
+       strcpy(strcurr,asctime(&tml));
+       rforecast_time=rcurr_time;
-         else if  (s2==-4) {
+       itmp = strlen(strcurr);
-           for (j=3,survp=0. ; j<=nlstate; j++)
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         strcurr[itmp-1]='\0';
-           lli= log(survp);
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-         }
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
+       for(niterf=10;niterf<=30;niterf+=10){
-         else if  (s2==-5) {
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-           for (j=1,survp=0. ; j<=2; j++)
+         forecast_time = *localtime(&rforecast_time);
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         strcpy(strfor,asctime(&forecast_time));
-           lli= log(survp);
+         itmp = strlen(strfor);
-         }
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
-         else{
+         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);
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+       }
-         }
+     }
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+     for (i=1;i<=n;i++) { /* For each direction i */
-         /*if(lli ==000.0)*/
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
-         /*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); */
+       fptt=(*fret);
-         ipmx +=1;
+ #ifdef DEBUG
-         sw += weight[i];
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       } /* end of wave */
+ #endif
-     } /* end of individual */
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
-   }  else if(mle==2){
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         /* because that direction will be replaced unless the gain del is small */
-           for (j=1;j<=nlstate+ndeath;j++){
+         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /* with the new direction. */
-           }
+         del=fabs(fptt-(*fret));
-         for(d=0; d<=dh[mi][i]; d++){
+         ibig=i;
-           newm=savm;
+       }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ #ifdef DEBUG
-           for (kk=1; kk<=cptcovage;kk++) {
+       printf("%d %.12e",i,(*fret));
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-           }
+       for (j=1;j<=n;j++) {
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         printf(" x(%d)=%.12e",j,xit[j]);
-           savm=oldm;
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-           oldm=newm;
+       }
-         } /* end mult */
+       for(j=1;j<=n;j++) {
+         printf(" p(%d)=%.12e",j,p[j]);
-         s1=s[mw[mi][i]][i];
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-         s2=s[mw[mi+1][i]][i];
+       }
-         bbh=(double)bh[mi][i]/(double)stepm;
+       printf("\n");
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       fprintf(ficlog,"\n");
-         ipmx +=1;
+ #endif
-         sw += weight[i];
+     } /* end loop on each direction i */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
-       } /* end of wave */
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
-     } /* end of individual */
+     /* New value of last point Pn is not computed, P(n-1) */
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* decreased of more than 3.84  */
-           for (j=1;j<=nlstate+ndeath;j++){
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /* By adding 10 parameters more the gain should be 18.31 */
-           }
-         for(d=0; d<dh[mi][i]; d++){
+       /* Starting the program with initial values given by a former maximization will simply change */
-           newm=savm;
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
-           for (kk=1; kk<=cptcovage;kk++) {
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef DEBUG
-           }
+       int k[2],l;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       k[0]=1;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       k[1]=-1;
-           savm=oldm;
+       printf("Max: %.12e",(*func)(p));
-           oldm=newm;
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-         } /* end mult */
+       for (j=1;j<=n;j++) {
+         printf(" %.12e",p[j]);
-         s1=s[mw[mi][i]][i];
+         fprintf(ficlog," %.12e",p[j]);
-         s2=s[mw[mi+1][i]][i];
+       }
-         bbh=(double)bh[mi][i]/(double)stepm;
+       printf("\n");
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       fprintf(ficlog,"\n");
-         ipmx +=1;
+       for(l=0;l<=1;l++) {
-         sw += weight[i];
+         for (j=1;j<=n;j++) {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-       } /* end of wave */
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     } /* end of individual */
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+         }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       for(mi=1; mi<= wav[i]-1; mi++){
+       }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ #endif
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       free_vector(xit,1,n);
-           }
+       free_vector(xits,1,n);
-         for(d=0; d<dh[mi][i]; d++){
+       free_vector(ptt,1,n);
-           newm=savm;
+       free_vector(pt,1,n);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       return;
-           for (kk=1; kk<=cptcovage;kk++) {
+     } /* enough precision */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     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) */
+       ptt[j]=2.0*p[j]-pt[j];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       xit[j]=p[j]-pt[j];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       pt[j]=p[j];
-           savm=oldm;
+     }
-           oldm=newm;
+     fptt=(*func)(ptt); /* f_3 */
-         } /* end mult */
+ #ifdef POWELLF1F3
+ #else
-         s1=s[mw[mi][i]][i];
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-         s2=s[mw[mi+1][i]][i];
+ #endif
-         if( s2 > nlstate){
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-         }else{
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-         }
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-         ipmx +=1;
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-         sw += weight[i];
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ #ifdef NRCORIGINAL
- /*      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]); */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-       } /* end of wave */
+ #else
-     } /* end of individual */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+       t= t- del*SQR(fp-fptt);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ #endif
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
-       for(mi=1; mi<= wav[i]-1; mi++){
+ #ifdef DEBUG
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       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 (j=1;j<=nlstate+ndeath;j++){
+       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);
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-           }
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-         for(d=0; d<dh[mi][i]; d++){
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-           newm=savm;
+       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);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-           for (kk=1; kk<=cptcovage;kk++) {
+ #endif
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ #ifdef POWELLORIGINAL
-           }
+       if (t < 0.0) { /* Then we use it for new direction */
+ #else
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
-           savm=oldm;
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-           oldm=newm;
+         fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
-         } /* end mult */
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+       }
-         s1=s[mw[mi][i]][i];
+       if (directest < 0.0) { /* Then we use it for new direction */
-         s2=s[mw[mi+1][i]][i];
+ #endif
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ #ifdef DEBUGLINMIN
-         ipmx +=1;
+         printf("Before linmin in direction P%d-P0\n",n);
-         sw += weight[i];
+         for (j=1;j<=n;j++) {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-       } /* end of wave */
+           if(j % ncovmodel == 0){
-     } /* end of individual */
+             printf("\n");
-   } /* End of if */
+             fprintf(ficlog,"\n");
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+           }
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         }
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ #endif
-   return -l;
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
- }
+ #ifdef DEBUGLINMIN
+         for (j=1;j<=n;j++) {
- /*************** log-likelihood *************/
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
- double funcone( double *x)
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
- {
+           if(j % ncovmodel == 0){
-   /* Same as likeli but slower because of a lot of printf and if */
+             printf("\n");
-   int i, ii, j, k, mi, d, kk;
+             fprintf(ficlog,"\n");
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+           }
-   double **out;
+         }
-   double lli; /* Individual log likelihood */
+ #endif
-   double llt;
+         for (j=1;j<=n;j++) {
-   int s1, s2;
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-   double bbh, survp;
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-   /*extern weight */
+         }
-   /* We are differentiating ll according to initial status */
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
+ #ifdef DEBUG
-   */
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   cov[1]=1.;
+         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++){
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+           printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         }
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         printf("\n");
-     for(mi=1; mi<= wav[i]-1; mi++){
+         fprintf(ficlog,"\n");
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+ #endif
-         for (j=1;j<=nlstate+ndeath;j++){
+       } /* end of t or directest negative */
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #ifdef POWELLF1F3
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #else
-         }
+     } /* end if (fptt < fp)  */
-       for(d=0; d<dh[mi][i]; d++){
+ #endif
-         newm=savm;
+   } /* loop iteration */
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ }
-         for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-         }
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ {
-         savm=oldm;
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-         oldm=newm;
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-       } /* end mult */
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-       s1=s[mw[mi][i]][i];
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-       s2=s[mw[mi+1][i]][i];
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-       bbh=(double)bh[mi][i]/(double)stepm;
+   /* Initial matrix pimij */
-       /* bias is positive if real duration
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-        * is higher than the multiple of stepm and negative otherwise.
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-        */
+   /*  0,                   0                  , 1} */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+   /*
-         lli=log(out[s1][s2] - savm[s1][s2]);
+    * and after some iteration: */
-       } else if  (s2==-2) {
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-         for (j=1,survp=0. ; j<=nlstate; j++)
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   /*  0,                   0                  , 1} */
-         lli= log(survp);
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
-       }else if (mle==1){
+   /* {0.51571254859325999, 0.4842874514067399, */
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+   /*  0.51326036147820708, 0.48673963852179264} */
-       } else if(mle==2){
+   /* If we start from prlim again, prlim tends to a constant matrix */
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-       } else if(mle==3){  /* exponential inter-extrapolation */
+   int i, ii,j,k;
-         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 */
+   double min, max, maxmin, maxmax,sumnew=0.;
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+   /* double **matprod2(); */ /* test */
-         lli=log(out[s1][s2]); /* Original formula */
+   double **out, cov[NCOVMAX+1], **pmij();
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+   double **newm;
-         lli=log(out[s1][s2]); /* Original formula */
+   double agefin, delaymax=100 ; /* Max number of years to converge */
-       } /* End of if */
+   int ncvloop=0;
-       ipmx +=1;
-       sw += weight[i];
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (j=1;j<=nlstate+ndeath;j++){
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       if(globpr){
+     }
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-  %11.6f %11.6f %11.6f ", \
+   cov[1]=1.;
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
-           llt +=ll[k]*gipmx/gsw;
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+     ncvloop++;
-         }
+     newm=savm;
-         fprintf(ficresilk," %10.6f\n", -llt);
+     /* Covariates have to be included here again */
-       }
+     cov[2]=agefin;
-     } /* end of wave */
+     if(nagesqr==1)
-   } /* end of individual */
+       cov[3]= agefin*agefin;;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+     for (k=1; k<=cptcovn;k++) {
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-   if(globpr==0){ /* First time we count the contributions and weights */
+       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
-     gipmx=ipmx;
+     }
-     gsw=sw;
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   }
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-   return -l;
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
- }
+     for (k=1; k<=cptcovprod;k++) /* Useless */
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
- /*************** function likelione ***********/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- {
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-   /* This routine should help understanding what is done with
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-      the selection of individuals/waves and
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-      to check the exact contribution to the likelihood.
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-      Plotting could be done.
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-    */
-   int k;
+     savm=oldm;
+     oldm=newm;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+     maxmax=0.;
-     strcpy(fileresilk,"ilk");
+     for(j=1;j<=nlstate;j++){
-     strcat(fileresilk,fileres);
+       min=1.;
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       max=0.;
-       printf("Problem with resultfile: %s\n", fileresilk);
+       for(i=1; i<=nlstate; i++) {
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+         sumnew=0;
-     }
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-     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");
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+         max=FMAX(max,prlim[i][j]);
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+         min=FMIN(min,prlim[i][j]);
-     for(k=1; k<=nlstate; k++)
+         printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min);
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+       }
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+       maxmin=(max-min)/(max+min)*2;
-   }
+       maxmax=FMAX(maxmax,maxmin);
+     } /* j loop */
-   *fretone=(*funcone)(p);
+     *ncvyear= (int)age- (int)agefin;
-   if(*globpri !=0){
+     printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear);
-     fclose(ficresilk);
+     if(maxmax < ftolpl){
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
-     fflush(fichtm);
+       return prlim;
-   }
+     }
-   return;
+   } /* age loop */
- }
+   printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
+ Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+ /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
- /*********** Maximum Likelihood Estimation ***************/
+   return prlim; /* should not reach here */
+ }
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
- {
+ /*************** transition probabilities ***************/
-   int i,j, iter;
-   double **xi;
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-   double fret;
+ {
-   double fretone; /* Only one call to likelihood */
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-   /*  char filerespow[FILENAMELENGTH];*/
+      computes the probability to be observed in state j being in state i by appying the
-   xi=matrix(1,npar,1,npar);
+      model to the ncovmodel covariates (including constant and age).
-   for (i=1;i<=npar;i++)
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-     for (j=1;j<=npar;j++)
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+      ncth covariate in the global vector x is given by the formula:
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-   strcpy(filerespow,"pow");
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-   strcat(filerespow,fileres);
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-     printf("Problem with resultfile: %s\n", filerespow);
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-   }
+   */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   double s1, lnpijopii;
-   for (i=1;i<=nlstate;i++)
+   /*double t34;*/
-     for(j=1;j<=nlstate+ndeath;j++)
+   int i,j, nc, ii, jj;
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   fprintf(ficrespow,"\n");
+     for(i=1; i<= nlstate; i++){
+       for(j=1; j<i;j++){
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-   free_matrix(xi,1,npar,1,npar);
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-   fclose(ficrespow);
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         }
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
- }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- /**** Computes Hessian and covariance matrix ***/
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(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); */
-   double  **a,**y,*x,pd;
+         }
-   double **hess;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   int i, j,jk;
+       }
-   int *indx;
+     }
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+     for(i=1; i<= nlstate; i++){
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+       s1=0;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+       for(j=1; j<i; j++){
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   double gompertz(double p[]);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   hess=matrix(1,npar,1,npar);
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   for (i=1;i<=npar;i++){
+       }
-     printf("%d",i);fflush(stdout);
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+       ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+       for(j=1; j<i; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     /*  printf(" %f ",p[i]);
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-   }
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
-   for (i=1;i<=npar;i++) {
-     for (j=1;j<=npar;j++)  {
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       if (j>i) {
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-         printf(".%d%d",i,j);fflush(stdout);
+         ps[ii][jj]=0;
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         ps[ii][ii]=1;
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       }
+     }
-         hess[j][i]=hess[i][j];
-         /*printf(" %lf ",hess[i][j]);*/
-       }
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     }
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-   }
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-   printf("\n");
+     /*   } */
-   fprintf(ficlog,"\n");
+     /*   printf("\n "); */
+     /* } */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+     /*
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   a=matrix(1,npar,1,npar);
+       goto end;*/
-   y=matrix(1,npar,1,npar);
+     return ps;
-   x=vector(1,npar);
+ }
-   indx=ivector(1,npar);
-   for (i=1;i<=npar;i++)
+ /**************** Product of 2 matrices ******************/
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   ludcmp(a,npar,indx,&pd);
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
+ {
-   for (j=1;j<=npar;j++) {
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-     for (i=1;i<=npar;i++) x[i]=0;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-     x[j]=1;
+   /* in, b, out are matrice of pointers which should have been initialized
-     lubksb(a,npar,indx,x);
+      before: only the contents of out is modified. The function returns
-     for (i=1;i<=npar;i++){
+      a pointer to pointers identical to out */
-       matcov[i][j]=x[i];
+   int i, j, k;
-     }
+   for(i=nrl; i<= nrh; i++)
-   }
+     for(k=ncolol; k<=ncoloh; k++){
+       out[i][k]=0.;
-   printf("\n#Hessian matrix#\n");
+       for(j=ncl; j<=nch; j++)
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+         out[i][k] +=in[i][j]*b[j][k];
-   for (i=1;i<=npar;i++) {
+     }
-     for (j=1;j<=npar;j++) {
+   return out;
-       printf("%.3e ",hess[i][j]);
+ }
-       fprintf(ficlog,"%.3e ",hess[i][j]);
-     }
-     printf("\n");
+ /************* Higher Matrix Product ***************/
-     fprintf(ficlog,"\n");
-   }
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ {
-   /* Recompute Inverse */
+   /* Computes the transition matrix starting at age 'age' over
-   for (i=1;i<=npar;i++)
+      'nhstepm*hstepm*stepm' months (i.e. until
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   ludcmp(a,npar,indx,&pd);
+      nhstepm*hstepm matrices.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   /*  printf("\n#Hessian matrix recomputed#\n");
+      (typically every 2 years instead of every month which is too big
+      for the memory).
-   for (j=1;j<=npar;j++) {
+      Model is determined by parameters x and covariates have to be
-     for (i=1;i<=npar;i++) x[i]=0;
+      included manually here.
-     x[j]=1;
-     lubksb(a,npar,indx,x);
+      */
-     for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+   int i, j, d, h, k;
-       printf("%.3e ",y[i][j]);
+   double **out, cov[NCOVMAX+1];
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   double **newm;
-     }
+   double agexact;
-     printf("\n");
-     fprintf(ficlog,"\n");
+   /* Hstepm could be zero and should return the unit matrix */
-   }
+   for (i=1;i<=nlstate+ndeath;i++)
-   */
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-   free_matrix(a,1,npar,1,npar);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-   free_matrix(y,1,npar,1,npar);
+     }
-   free_vector(x,1,npar);
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   free_ivector(indx,1,npar);
+   for(h=1; h <=nhstepm; h++){
-   free_matrix(hess,1,npar,1,npar);
+     for(d=1; d <=hstepm; d++){
+       newm=savm;
+       /* Covariates have to be included here again */
- }
+       cov[1]=1.;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
- /*************** hessian matrix ****************/
+       cov[2]=agexact;
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+       if(nagesqr==1)
- {
+         cov[3]= agexact*agexact;
-   int i;
+       for (k=1; k<=cptcovn;k++)
-   int l=1, lmax=20;
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-   double k1,k2;
+         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-   double p2[NPARMAX+1];
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-   double res;
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-   double fx;
+         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
-   int k=0,kmax=10;
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-   double l1;
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-   fx=func(x);
-   for (i=1;i<=npar;i++) p2[i]=x[i];
-   for(l=0 ; l <=lmax; l++){
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-     l1=pow(10,l);
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-     delts=delt;
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-     for(k=1 ; k <kmax; k=k+1){
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-       delt = delta*(l1*k);
+       savm=oldm;
-       p2[theta]=x[theta] +delt;
+       oldm=newm;
-       k1=func(p2)-fx;
+     }
-       p2[theta]=x[theta]-delt;
+     for(i=1; i<=nlstate+ndeath; i++)
-       k2=func(p2)-fx;
+       for(j=1;j<=nlstate+ndeath;j++) {
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         po[i][j][h]=newm[i][j];
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
- #ifdef DEBUG
+     /*printf("h=%d ",h);*/
-       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);
+   } /* end h */
-       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);
+ /*     printf("\n H=%d \n",h); */
- #endif
+   return po;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+ }
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-         k=kmax;
+ #ifdef NLOPT
-       }
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+   double fret;
-         k=kmax; l=lmax*10.;
+   double *xt;
-       }
+   int j;
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   myfunc_data *d2 = (myfunc_data *) pd;
-         delts=delt;
+ /* xt = (p1-1); */
-       }
+   xt=vector(1,n);
-     }
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   }
-   delti[theta]=delts;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-   return res;
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
+   printf("Function = %.12lf ",fret);
- }
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
+   printf("\n");
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+  free_vector(xt,1,n);
- {
+   return fret;
-   int i;
+ }
-   int l=1, l1, lmax=20;
+ #endif
-   double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+ /*************** log-likelihood *************/
-   int k;
+ double func( double *x)
+ {
-   fx=func(x);
+   int i, ii, j, k, mi, d, kk;
-   for (k=1; k<=2; k++) {
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+   double **out;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   double sw; /* Sum of weights */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   double lli; /* Individual log likelihood */
-     k1=func(p2)-fx;
+   int s1, s2;
+   double bbh, survp;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   long ipmx;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   double agexact;
-     k2=func(p2)-fx;
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   /*for(i=1;i<imx;i++)
-     k3=func(p2)-fx;
+     printf(" %d\n",s[4][i]);
+   */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   ++countcallfunc;
-     k4=func(p2)-fx;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+   cov[1]=1.;
- #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);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     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
+   if(mle==1){
-   }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   return res;
+       /* Computes the values of the ncovmodel covariates of the model
- }
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
- /************** Inverse of matrix **************/
+          to be observed in j being in i according to the model.
- void ludcmp(double **a, int n, int *indx, double *d)
+        */
- {
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-   int i,imax,j,k;
+           cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   double big,dum,sum,temp;
+       }
-   double *vv;
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-   vv=vector(1,n);
+          has been calculated etc */
-   *d=1.0;
+       for(mi=1; mi<= wav[i]-1; mi++){
-   for (i=1;i<=n;i++) {
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     big=0.0;
+           for (j=1;j<=nlstate+ndeath;j++){
-     for (j=1;j<=n;j++)
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+           }
-     vv[i]=1.0/big;
+         for(d=0; d<dh[mi][i]; d++){
-   }
+           newm=savm;
-   for (j=1;j<=n;j++) {
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     for (i=1;i<j;i++) {
+           cov[2]=agexact;
-       sum=a[i][j];
+           if(nagesqr==1)
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+             cov[3]= agexact*agexact;
-       a[i][j]=sum;
+           for (kk=1; kk<=cptcovage;kk++) {
-     }
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-     big=0.0;
+           }
-     for (i=j;i<=n;i++) {
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       sum=a[i][j];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       for (k=1;k<j;k++)
+           savm=oldm;
-         sum -= a[i][k]*a[k][j];
+           oldm=newm;
-       a[i][j]=sum;
+         } /* end mult */
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
-         big=dum;
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         imax=i;
+         /* 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
-     if (j != imax) {
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-       for (k=1;k<=n;k++) {
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         dum=a[imax][k];
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         a[imax][k]=a[j][k];
+          * probability in order to take into account the bias as a fraction of the way
-         a[j][k]=dum;
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-       }
+          * -stepm/2 to stepm/2 .
-       *d = -(*d);
+          * For stepm=1 the results are the same as for previous versions of Imach.
-       vv[imax]=vv[j];
+          * For stepm > 1 the results are less biased than in previous versions.
-     }
+          */
-     indx[j]=imax;
+         s1=s[mw[mi][i]][i];
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+         s2=s[mw[mi+1][i]][i];
-     if (j != n) {
+         bbh=(double)bh[mi][i]/(double)stepm;
-       dum=1.0/(a[j][j]);
+         /* bias bh is positive if real duration
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+          * is higher than the multiple of stepm and negative otherwise.
-     }
+          */
-   }
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-   free_vector(vv,1,n);  /* Doesn't work */
+         if( s2 > nlstate){
- ;
+           /* i.e. if s2 is a death state and if the date of death is known
- }
+              then the contribution to the likelihood is the probability to
+              die between last step unit time and current  step unit time,
- void lubksb(double **a, int n, int *indx, double b[])
+              which is also equal to probability to die before dh
- {
+              minus probability to die before dh-stepm .
-   int i,ii=0,ip,j;
+              In version up to 0.92 likelihood was computed
-   double sum;
+         as if date of death was unknown. Death was treated as any other
+         health state: the date of the interview describes the actual state
-   for (i=1;i<=n;i++) {
+         and not the date of a change in health state. The former idea was
-     ip=indx[i];
+         to consider that at each interview the state was recorded
-     sum=b[ip];
+         (healthy, disable or death) and IMaCh was corrected; but when we
-     b[ip]=b[i];
+         introduced the exact date of death then we should have modified
-     if (ii)
+         the contribution of an exact death to the likelihood. This new
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+         contribution is smaller and very dependent of the step unit
-     else if (sum) ii=i;
+         stepm. It is no more the probability to die between last interview
-     b[i]=sum;
+         and month of death but the probability to survive from last
-   }
+         interview up to one month before death multiplied by the
-   for (i=n;i>=1;i--) {
+         probability to die within a month. Thanks to Chris
-     sum=b[i];
+         Jackson for correcting this bug.  Former versions increased
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+         mortality artificially. The bad side is that we add another loop
-     b[i]=sum/a[i][i];
+         which slows down the processing. The difference can be up to 10%
-   }
+         lower mortality.
- }
+           */
+         /* If, at the beginning of the maximization mostly, the
- void pstamp(FILE *fichier)
+            cumulative probability or probability to be dead is
- {
+            constant (ie = 1) over time d, the difference is equal to
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+.  out[s1][3] = savm[s1][3]: probability, being at state
- }
+            s1 at precedent wave, to be dead a month before current
+            wave is equal to probability, being at state s1 at
- /************ Frequencies ********************/
+            precedent wave, to be dead at mont of the current
- 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[])
+            wave. Then the observed probability (that this person died)
- {  /* Some frequencies */
+            is null according to current estimated parameter. In fact,
+            it should be very low but not zero otherwise the log go to
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+            infinity.
-   int first;
+         */
-   double ***freq; /* Frequencies */
+ /* #ifdef INFINITYORIGINAL */
-   double *pp, **prop;
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+ /* #else */
-   char fileresp[FILENAMELENGTH];
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
+ /*          lli=log(mytinydouble); */
-   pp=vector(1,nlstate);
+ /*        else */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-   strcpy(fileresp,"p");
+ /* #endif */
-   strcat(fileresp,fileres);
+             lli=log(out[s1][s2] - savm[s1][s2]);
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+         } else if  (s2==-2) {
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+           for (j=1,survp=0. ; j<=nlstate; j++)
-     exit(0);
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   }
+           /*survp += out[s1][j]; */
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+           lli= log(survp);
-   j1=0;
+         }
-   j=cptcoveff;
+         else if  (s2==-4) {
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   first=1;
+           lli= log(survp);
+         }
-   for(k1=1; k1<=j;k1++){
-     for(i1=1; i1<=ncodemax[k1];i1++){
+         else if  (s2==-5) {
-       j1++;
+           for (j=1,survp=0. ; j<=2; j++)
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         scanf("%d", i);*/
+           lli= log(survp);
-       for (i=-5; i<=nlstate+ndeath; i++)
+         }
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           for(m=iagemin; m <= iagemax+3; m++)
+         else{
-             freq[i][jk][m]=0;
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-     for (i=1; i<=nlstate; i++)
+         }
-       for(m=iagemin; m <= iagemax+3; m++)
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         prop[i][m]=0;
+         /*if(lli ==000.0)*/
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-       dateintsum=0;
+         ipmx +=1;
-       k2cpt=0;
+         sw += weight[i];
-       for (i=1; i<=imx; i++) {
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         bool=1;
+         /* if (lli < log(mytinydouble)){ */
-         if  (cptcovn>0) {
+         /*   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); */
-           for (z1=1; z1<=cptcoveff; z1++)
+         /*   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]); */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+         /* } */
-               bool=0;
+       } /* end of wave */
-         }
+     } /* end of individual */
-         if (bool==1){
+   }  else if(mle==2){
-           for(m=firstpass; m<=lastpass; m++){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+       for(mi=1; mi<= wav[i]-1; mi++){
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+           for (j=1;j<=nlstate+ndeath;j++){
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-               if (m<lastpass) {
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+           }
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+         for(d=0; d<=dh[mi][i]; d++){
-               }
+           newm=savm;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+           cov[2]=agexact;
-                 dateintsum=dateintsum+k2;
+           if(nagesqr==1)
-                 k2cpt++;
+             cov[3]= agexact*agexact;
-               }
+           for (kk=1; kk<=cptcovage;kk++) {
-               /*}*/
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
-         }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+           oldm=newm;
-       pstamp(ficresp);
+         } /* end mult */
-       if  (cptcovn>0) {
-         fprintf(ficresp, "\n#********** Variable ");
+         s1=s[mw[mi][i]][i];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         s2=s[mw[mi+1][i]][i];
-         fprintf(ficresp, "**********\n#");
+         bbh=(double)bh[mi][i]/(double)stepm;
-       }
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-       for(i=1; i<=nlstate;i++)
+         ipmx +=1;
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+         sw += weight[i];
-       fprintf(ficresp, "\n");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
-       for(i=iagemin; i <= iagemax+3; i++){
+     } /* end of individual */
-         if(i==iagemax+3){
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-           fprintf(ficlog,"Total");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         }else{
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-           if(first==1){
+       for(mi=1; mi<= wav[i]-1; mi++){
-             first=0;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-             printf("See log file for details...\n");
+           for (j=1;j<=nlstate+ndeath;j++){
-           }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           fprintf(ficlog,"Age %d", i);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+           }
-         for(jk=1; jk <=nlstate ; jk++){
+         for(d=0; d<dh[mi][i]; d++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+           newm=savm;
-             pp[jk] += freq[jk][m][i];
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         }
+           cov[2]=agexact;
-         for(jk=1; jk <=nlstate ; jk++){
+           if(nagesqr==1)
-           for(m=-1, pos=0; m <=0 ; m++)
+             cov[3]= agexact*agexact;
-             pos += freq[jk][m][i];
+           for (kk=1; kk<=cptcovage;kk++) {
-           if(pp[jk]>=1.e-10){
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-             if(first==1){
+           }
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-             }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           savm=oldm;
-           }else{
+           oldm=newm;
-             if(first==1)
+         } /* end mult */
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         s1=s[mw[mi][i]][i];
-           }
+         s2=s[mw[mi+1][i]][i];
-         }
+         bbh=(double)bh[mi][i]/(double)stepm;
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         for(jk=1; jk <=nlstate ; jk++){
+         ipmx +=1;
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+         sw += weight[i];
-             pp[jk] += freq[jk][m][i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         }
+       } /* end of wave */
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+     } /* end of individual */
-           pos += pp[jk];
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-           posprop += prop[jk][i];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         }
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-         for(jk=1; jk <=nlstate ; jk++){
+       for(mi=1; mi<= wav[i]-1; mi++){
-           if(pos>=1.e-5){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-             if(first==1)
+           for (j=1;j<=nlstate+ndeath;j++){
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           }else{
+           }
-             if(first==1)
+         for(d=0; d<dh[mi][i]; d++){
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           newm=savm;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           }
+           cov[2]=agexact;
-           if( i <= iagemax){
+           if(nagesqr==1)
-             if(pos>=1.e-5){
+             cov[3]= agexact*agexact;
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+           for (kk=1; kk<=cptcovage;kk++) {
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*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]);*/
+           }
-             }
-             else
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           }
+           savm=oldm;
-         }
+           oldm=newm;
+         } /* end mult */
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
-           for(m=-1; m <=nlstate+ndeath; m++)
+         s1=s[mw[mi][i]][i];
-             if(freq[jk][m][i] !=0 ) {
+         s2=s[mw[mi+1][i]][i];
-             if(first==1)
+         if( s2 > nlstate){
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+         }else{
-             }
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         if(i <= iagemax)
+         }
-           fprintf(ficresp,"\n");
+         ipmx +=1;
-         if(first==1)
+         sw += weight[i];
-           printf("Others in log...\n");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         fprintf(ficlog,"\n");
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-       }
+       } /* end of wave */
-     }
+     } /* end of individual */
-   }
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   dateintmean=dateintsum/k2cpt;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-   fclose(ficresp);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   free_vector(pp,1,nlstate);
+           for (j=1;j<=nlstate+ndeath;j++){
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /* End of Freq */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
+           }
+         for(d=0; d<dh[mi][i]; d++){
- /************ Prevalence ********************/
+           newm=savm;
- 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)
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
- {
+           cov[2]=agexact;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+           if(nagesqr==1)
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+             cov[3]= agexact*agexact;
-      We still use firstpass and lastpass as another selection.
+           for (kk=1; kk<=cptcovage;kk++) {
-   */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           }
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
-   double ***freq; /* Frequencies */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   double *pp, **prop;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   double pos,posprop;
+           savm=oldm;
-   double  y2; /* in fractional years */
+           oldm=newm;
-   int iagemin, iagemax;
+         } /* end mult */
-   iagemin= (int) agemin;
+         s1=s[mw[mi][i]][i];
-   iagemax= (int) agemax;
+         s2=s[mw[mi+1][i]][i];
-   /*pp=vector(1,nlstate);*/
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         ipmx +=1;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+         sw += weight[i];
-   j1=0;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-   j=cptcoveff;
+       } /* end of wave */
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+     } /* end of individual */
+   } /* End of if */
-   for(k1=1; k1<=j;k1++){
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       j1++;
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
-       for (i=1; i<=nlstate; i++)
+ }
-         for(m=iagemin; m <= iagemax+3; m++)
-           prop[i][m]=0.0;
+ /*************** log-likelihood *************/
+ double funcone( double *x)
-       for (i=1; i<=imx; i++) { /* Each individual */
+ {
-         bool=1;
+   /* Same as likeli but slower because of a lot of printf and if */
-         if  (cptcovn>0) {
+   int i, ii, j, k, mi, d, kk;
-           for (z1=1; z1<=cptcoveff; z1++)
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   double **out;
-               bool=0;
+   double lli; /* Individual log likelihood */
-         }
+   double llt;
-         if (bool==1) {
+   int s1, s2;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+   double bbh, survp;
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+   double agexact;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+   /*extern weight */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   /* We are differentiating ll according to initial status */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+   /*for(i=1;i<imx;i++)
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+     printf(" %d\n",s[4][i]);
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+   */
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   cov[1]=1.;
-                 prop[s[m][i]][iagemax+3] += weight[i];
-               }
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-             }
-           } /* end selection of waves */
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         }
+     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
-       }
+     for(mi=1; mi<= wav[i]-1; mi++){
-       for(i=iagemin; i <= iagemax+3; i++){
+       for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=nlstate+ndeath;j++){
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           posprop += prop[jk][i];
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
          }
+       for(d=0; d<dh[mi][i]; d++){
-         for(jk=1; jk <=nlstate ; jk++){
+         newm=savm;
-           if( i <=  iagemax){
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-             if(posprop>=1.e-5){
+         cov[2]=agexact;
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+         if(nagesqr==1)
-             }
+           cov[3]= agexact*agexact;
-           }
+         for (kk=1; kk<=cptcovage;kk++) {
-         }/* end jk */
+           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-       }/* end i */
+         }
-     } /* end i1 */
-   } /* end k1 */
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /*free_vector(pp,1,nlstate);*/
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
- }  /* End of prevalence */
+         savm=oldm;
+         oldm=newm;
- /************* Waves Concatenation ***************/
+       } /* end mult */
- 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)
+       s1=s[mw[mi][i]][i];
- {
+       s2=s[mw[mi+1][i]][i];
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       bbh=(double)bh[mi][i]/(double)stepm;
-      Death is a valid wave (if date is known).
+       /* bias is positive if real duration
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+        * is higher than the multiple of stepm and negative otherwise.
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+        */
-      and mw[mi+1][i]. dh depends on stepm.
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-      */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
-   int i, mi, m;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-      double sum=0., jmean=0.;*/
+         lli= log(survp);
-   int first;
+       }else if (mle==1){
-   int j, k=0,jk, ju, jl;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   double sum=0.;
+       } else if(mle==2){
-   first=0;
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   jmin=1e+5;
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   jmax=-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 */
-   jmean=0.;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   for(i=1; i<=imx; i++){
+         lli=log(out[s1][s2]); /* Original formula */
-     mi=0;
+       } else{  /* mle=0 back to 1 */
-     m=firstpass;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     while(s[m][i] <= nlstate){
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       } /* End of if */
-         mw[++mi][i]=m;
+       ipmx +=1;
-       if(m >=lastpass)
+       sw += weight[i];
-         break;
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       else
+       /*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]); */
-         m++;
+       if(globpr){
-     }/* end while */
+         fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
-     if (s[m][i] > nlstate){
+  %11.6f %11.6f %11.6f ", \
-       mi++;     /* Death is another wave */
+                 num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-       /* if(mi==0)  never been interviewed correctly before death */
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-          /* Only death is a correct wave */
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-       mw[mi][i]=m;
+           llt +=ll[k]*gipmx/gsw;
-     }
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
-     wav[i]=mi;
+         fprintf(ficresilk," %10.6f\n", -llt);
-     if(mi==0){
+       }
-       nbwarn++;
+     } /* end of wave */
-       if(first==0){
+   } /* end of individual */
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-         first=1;
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       }
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-       if(first==1){
+   if(globpr==0){ /* First time we count the contributions and weights */
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+     gipmx=ipmx;
-       }
+     gsw=sw;
-     } /* end mi==0 */
+   }
-   } /* End individuals */
+   return -l;
+ }
-   for(i=1; i<=imx; i++){
-     for(mi=1; mi<wav[i];mi++){
-       if (stepm <=0)
+ /*************** function likelione ***********/
-         dh[mi][i]=1;
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-       else{
+ {
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+   /* This routine should help understanding what is done with
-           if (agedc[i] < 2*AGESUP) {
+      the selection of individuals/waves and
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+      to check the exact contribution to the likelihood.
-             if(j==0) j=1;  /* Survives at least one month after exam */
+      Plotting could be done.
-             else if(j<0){
+    */
-               nberr++;
+   int k;
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               j=1; /* Temporary Dangerous patch */
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-               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);
+     strcpy(fileresilk,"ILK_");
-               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]);
+     strcat(fileresilk,fileresu);
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-             }
+       printf("Problem with resultfile: %s\n", fileresilk);
-             k=k+1;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-             if (j >= jmax){
+     }
-               jmax=j;
+     fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-               ijmax=i;
+     fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %weight 2wlli out sav ");
-             }
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-             if (j <= jmin){
+     for(k=1; k<=nlstate; k++)
-               jmin=j;
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-               ijmin=i;
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-             }
+   }
-             sum=sum+j;
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   *fretone=(*funcone)(p);
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   if(*globpri !=0){
-           }
+     fclose(ficresilk);
-         }
+     if (mle ==0)
-         else{
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+     else if(mle >=1)
- /*        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(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
+     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-           k=k+1;
-           if (j >= jmax) {
+       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
-             jmax=j;
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-             ijmax=i;
+       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
-           }
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
-           else if (j <= jmin){
+       fflush(fichtm);
-             jmin=j;
-             ijmin=i;
+       for (k=1; k<= nlstate ; k++) {
-           }
+         fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+       }
-           if(j<0){
+   }
-             nberr++;
+   return;
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ }
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           }
-           sum=sum+j;
+ /*********** Maximum Likelihood Estimation ***************/
-         }
-         jk= j/stepm;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-         jl= j -jk*stepm;
+ {
-         ju= j -(jk+1)*stepm;
+   int i,j, iter=0;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   double **xi;
-           if(jl==0){
+   double fret;
-             dh[mi][i]=jk;
+   double fretone; /* Only one call to likelihood */
-             bh[mi][i]=0;
+   /*  char filerespow[FILENAMELENGTH];*/
-           }else{ /* We want a negative bias in order to only have interpolation ie
-                   * at the price of an extra matrix product in likelihood */
+ #ifdef NLOPT
-             dh[mi][i]=jk+1;
+   int creturn;
-             bh[mi][i]=ju;
+   nlopt_opt opt;
-           }
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-         }else{
+   double *lb;
-           if(jl <= -ju){
+   double minf; /* the minimum objective value, upon return */
-             dh[mi][i]=jk;
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-             bh[mi][i]=jl;       /* bias is positive if real duration
+   myfunc_data dinst, *d = &dinst;
-                                  * is higher than the multiple of stepm and negative otherwise.
+ #endif
-                                  */
-           }
-           else{
+   xi=matrix(1,npar,1,npar);
-             dh[mi][i]=jk+1;
+   for (i=1;i<=npar;i++)
-             bh[mi][i]=ju;
+     for (j=1;j<=npar;j++)
-           }
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-           if(dh[mi][i]==0){
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-             dh[mi][i]=1; /* At least one step */
+   strcpy(filerespow,"POW_");
-             bh[mi][i]=ju; /* At least one step */
+   strcat(filerespow,fileres);
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-           }
+     printf("Problem with resultfile: %s\n", filerespow);
-         } /* end if mle */
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       }
+   }
-     } /* end wave */
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   }
+   for (i=1;i<=nlstate;i++)
-   jmean=sum/k;
+     for(j=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);
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   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);
+   fprintf(ficrespow,"\n");
-  }
+ #ifdef POWELL
+   powell(p,xi,npar,ftol,&iter,&fret,func);
- /*********** Tricode ****************************/
+ #endif
- void tricode(int *Tvar, int **nbcode, int imx)
- {
+ #ifdef NLOPT
+ #ifdef NEWUOA
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-   int cptcode=0;
+ #else
-   cptcoveff=0;
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+ #endif
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   lb=vector(0,npar-1);
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   nlopt_set_initial_step1(opt, 0.1);
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
-                                modality*/
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+   d->function = func;
-       Ndum[ij]++; /*store the modality */
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+   nlopt_set_min_objective(opt, myfunc, d);
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+   nlopt_set_xtol_rel(opt, ftol);
-                                        Tvar[j]. If V=sex and male is 0 and
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-                                        female is 1, then  cptcode=1.*/
+     printf("nlopt failed! %d\n",creturn);
-     }
+   }
+   else {
-     for (i=0; i<=cptcode; i++) {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-       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 */
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-     }
+     iter=1; /* not equal */
+   }
-     ij=1;
+   nlopt_destroy(opt);
-     for (i=1; i<=ncodemax[j]; i++) {
+ #endif
-       for (k=0; k<= maxncov; k++) {
+   free_matrix(xi,1,npar,1,npar);
-         if (Ndum[k] != 0) {
+   fclose(ficrespow);
-           nbcode[Tvar[j]][ij]=k;
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-           /* 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; */
+   fprintf(ficlog,"\n#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));
-           ij++;
-         }
+ }
-         if (ij > ncodemax[j]) break;
-       }
+ /**** Computes Hessian and covariance matrix ***/
-     }
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-   }
+ {
+   double  **a,**y,*x,pd;
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   /* double **hess; */
+   int i, j;
-  for (i=1; i<=ncovmodel-2; i++) {
+   int *indx;
-    /* 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];
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-    Ndum[ij]++;
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
-  }
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-  ij=1;
+   double gompertz(double p[]);
-  for (i=1; i<= maxncov; i++) {
+   /* hess=matrix(1,npar,1,npar); */
-    if((Ndum[i]!=0) && (i<=ncovcol)){
-      Tvaraff[ij]=i; /*For printing */
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-      ij++;
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-    }
+   for (i=1;i<=npar;i++){
-  }
+     printf("%d-",i);fflush(stdout);
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
-  cptcoveff=ij-1; /*Number of simple covariates*/
- }
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- /*********** Health Expectancies ****************/
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+   }
- {
+   for (i=1;i<=npar;i++) {
-   /* Health expectancies, no variances */
+     for (j=1;j<=npar;j++)  {
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+       if (j>i) {
-   double age, agelim, hf;
+         printf(".%d-%d",i,j);fflush(stdout);
-   double ***p3mat;
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-   double eip;
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
-   pstamp(ficreseij);
+         hess[j][i]=hess[i][j];
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+         /*printf(" %lf ",hess[i][j]);*/
-   fprintf(ficreseij,"# Age");
+       }
-   for(i=1; i<=nlstate;i++){
+     }
-     for(j=1; j<=nlstate;j++){
+   }
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   printf("\n");
-     }
+   fprintf(ficlog,"\n");
-     fprintf(ficreseij," e%1d. ",i);
-   }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   fprintf(ficreseij,"\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+   a=matrix(1,npar,1,npar);
-   if(estepm < stepm){
+   y=matrix(1,npar,1,npar);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   x=vector(1,npar);
-   }
+   indx=ivector(1,npar);
-   else  hstepm=estepm;
+   for (i=1;i<=npar;i++)
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-    * This is mainly to measure the difference between two models: for example
+   ludcmp(a,npar,indx,&pd);
-    * 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
+   for (j=1;j<=npar;j++) {
-    * progression in between and thus overestimating or underestimating according
+     for (i=1;i<=npar;i++) x[i]=0;
-    * to the curvature of the survival function. If, for the same date, we
+     x[j]=1;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+     lubksb(a,npar,indx,x);
-    * to compare the new estimate of Life expectancy with the same linear
+     for (i=1;i<=npar;i++){
-    * hypothesis. A more precise result, taking into account a more precise
+       matcov[i][j]=x[i];
-    * curvature will be obtained if estepm is as small as stepm. */
+     }
+   }
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   printf("\n#Hessian matrix#\n");
-      nhstepm is the number of hstepm from age to agelim
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-      nstepm is the number of stepm from age to agelin.
+   for (i=1;i<=npar;i++) {
-      Look at hpijx to understand the reason of that which relies in memory size
+     for (j=1;j<=npar;j++) {
-      and note for a fixed period like estepm months */
+       printf("%.6e ",hess[i][j]);
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       fprintf(ficlog,"%.6e ",hess[i][j]);
-      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
+     printf("\n");
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     fprintf(ficlog,"\n");
-      results. So we changed our mind and took the option of the best precision.
+   }
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
-   agelim=AGESUP;
+   /* for (i=1;i<=npar;i++) {  */
-   /* If stepm=6 months */
+   /*   for (j=1;j<=npar;j++) {  */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+   /*     printf("%.6e ",matcov[i][j]); */
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
- /* nhstepm age range expressed in number of stepm */
+   /*   printf("\n"); */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /*   fprintf(ficlog,"\n"); */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* } */
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   /* Recompute Inverse */
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* for (i=1;i<=npar;i++) */
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   for (age=bage; age<=fage; age ++){
+   /* ludcmp(a,npar,indx,&pd); */
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   /* for (j=1;j<=npar;j++) { */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
-     printf("%d|",(int)age);fflush(stdout);
+   /*   lubksb(a,npar,indx,x); */
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   /*   for (i=1;i<=npar;i++){  */
+   /*     y[i][j]=x[i]; */
+   /*     printf("%.3e ",y[i][j]); */
-     /* Computing expectancies */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
-     for(i=1; i<=nlstate;i++)
+   /*   } */
-       for(j=1; j<=nlstate;j++)
+   /*   printf("\n"); */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   /*   fprintf(ficlog,"\n"); */
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+   /* } */
-           /*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]);*/
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
-         }
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-     fprintf(ficreseij,"%3.0f",age );
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
-     for(i=1; i<=nlstate;i++){
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
-       eip=0;
-       for(j=1; j<=nlstate;j++){
+   for (j=1;j<=npar;j++) {
-         eip +=eij[i][j][(int)age];
+     for (i=1;i<=npar;i++){
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       printf("%.2f ",y[i][j]);
-       }
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       fprintf(ficreseij,"%9.4f", eip );
+     }
-     }
+     printf("\n");
-     fprintf(ficreseij,"\n");
+     fprintf(ficlog,"\n");
+   }
-   }
+ #endif
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   printf("\n");
+   free_matrix(a,1,npar,1,npar);
-   fprintf(ficlog,"\n");
+   free_matrix(y,1,npar,1,npar);
+   free_vector(x,1,npar);
- }
+   free_ivector(indx,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
- 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[] )
- {
+ }
-   /* Covariances of health expectancies eij and of total life expectancies according
-    to initial status i, ei. .
+ /*************** hessian matrix ****************/
-   */
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
-   double age, agelim, hf;
+   int i;
-   double ***p3matp, ***p3matm, ***varhe;
+   int l=1, lmax=20;
-   double **dnewm,**doldm;
+   double k1,k2, res, fx;
-   double *xp, *xm;
+   double p2[MAXPARM+1]; /* identical to x */
-   double **gp, **gm;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double ***gradg, ***trgradg;
+   int k=0,kmax=10;
-   int theta;
+   double l1;
-   double eip, vip;
+   fx=func(x);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   xp=vector(1,npar);
+     l1=pow(10,l);
-   xm=vector(1,npar);
+     delts=delt;
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+     for(k=1 ; k <kmax; k=k+1){
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+       delt = delta*(l1*k);
+       p2[theta]=x[theta] +delt;
-   pstamp(ficresstdeij);
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+       p2[theta]=x[theta]-delt;
-   fprintf(ficresstdeij,"# Age");
+       k2=func(p2)-fx;
-   for(i=1; i<=nlstate;i++){
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-     for(j=1; j<=nlstate;j++)
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-     fprintf(ficresstdeij," e%1d. ",i);
+ #ifdef DEBUGHESSII
-   }
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   fprintf(ficresstdeij,"\n");
+       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
-   pstamp(ficrescveij);
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   fprintf(ficrescveij,"# Age");
+         k=kmax;
-   for(i=1; i<=nlstate;i++)
+       }
-     for(j=1; j<=nlstate;j++){
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-       cptj= (j-1)*nlstate+i;
+         k=kmax; l=lmax*10;
-       for(i2=1; i2<=nlstate;i2++)
+       }
-         for(j2=1; j2<=nlstate;j2++){
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-           cptj2= (j2-1)*nlstate+i2;
+         delts=delt;
-           if(cptj2 <= cptj)
+       }
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+     } /* End loop k */
-         }
+   }
-     }
+   delti[theta]=delts;
-   fprintf(ficrescveij,"\n");
+   return res;
-   if(estepm < stepm){
+ }
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-   else  hstepm=estepm;
+ {
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   int i;
-    * This is mainly to measure the difference between two models: for example
+   int l=1, lmax=20;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   double k1,k2,k3,k4,res,fx;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   double p2[MAXPARM+1];
-    * progression in between and thus overestimating or underestimating according
+   int k, kmax=1;
-    * to the curvature of the survival function. If, for the same date, we
+   double v1, v2, cv12, lc1, lc2;
-    * 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
+   fx=func(x);
-    * hypothesis. A more precise result, taking into account a more precise
+   for (k=1; k<=kmax; k=k+10) {
-    * curvature will be obtained if estepm is as small as stepm. */
+     for (i=1;i<=npar;i++) p2[i]=x[i];
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+     k1=func(p2)-fx;
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-      Look at hpijx to understand the reason of that which relies in memory size
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
-      and note for a fixed period like estepm months */
+     k2=func(p2)-fx;
-   /* 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
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-      means that if the survival funtion is printed only each two years of age and if
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     k3=func(p2)-fx;
-      results. So we changed our mind and took the option of the best precision.
-   */
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
+     k4=func(p2)-fx;
-   /* If stepm=6 months */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
-   /* nhstepm age range expressed in number of stepm */
+     if(k1*k2*k3*k4 <0.){
-   agelim=AGESUP;
+       kmax=kmax+10;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       if(kmax >=10){
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
-   /* if (stepm >= YEARM) hstepm=1;*/
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     }
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+ #ifdef DEBUGHESSIJ
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+     v1=hess[thetai][thetai];
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+     v2=hess[thetaj][thetaj];
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+     cv12=res;
+     /* Computing eigen value of Hessian matrix */
-   for (age=bage; age<=fage; age ++){
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+     if ((lc2 <0) || (lc1 <0) ){
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-     /* Computing  Variances of health expectancies */
+     }
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+ #endif
-        decrease memory allocation */
+   }
-     for(theta=1; theta <=npar; theta++){
+   return res;
-       for(i=1; i<=npar; i++){
+ }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
-       }
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+ /* { */
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+ /*   int i; */
+ /*   int l=1, lmax=20; */
-       for(j=1; j<= nlstate; j++){
+ /*   double k1,k2,k3,k4,res,fx; */
-         for(i=1; i<=nlstate; i++){
+ /*   double p2[MAXPARM+1]; */
-           for(h=0; h<=nhstepm-1; h++){
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+ /*   int k=0,kmax=10; */
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+ /*   double l1; */
-           }
-         }
+ /*   fx=func(x); */
-       }
+ /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
+ /*     l1=pow(10,l); */
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+ /*     delts=delt; */
-         for(h=0; h<=nhstepm-1; h++){
+ /*     for(k=1 ; k <kmax; k=k+1){ */
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+ /*       delt = delti*(l1*k); */
-         }
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
-     }/* End theta */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k1=func(p2)-fx; */
-     for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*nlstate;j++)
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
-         for(theta=1; theta <=npar; theta++)
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+ /*       k2=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+ /*       k3=func(p2)-fx; */
-         varhe[ij][ji][(int)age] =0.;
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
-      printf("%d|",(int)age);fflush(stdout);
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+ /*       k4=func(p2)-fx; */
-      for(h=0;h<=nhstepm-1;h++){
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
-       for(k=0;k<=nhstepm-1;k++){
+ /* #ifdef DEBUGHESSIJ */
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+ /*       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); */
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+ /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+ /* #endif */
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+ /*      k=kmax; */
-       }
+ /*       } */
-     }
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
+ /*      k=kmax; l=lmax*10; */
-     /* Computing expectancies */
+ /*       } */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
-     for(i=1; i<=nlstate;i++)
+ /*      delts=delt; */
-       for(j=1; j<=nlstate;j++)
+ /*       } */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+ /*     } /\* End loop k *\/ */
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+ /*   } */
+ /*   delti[theta]=delts; */
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+ /*   return res;  */
+ /* } */
-         }
-     fprintf(ficresstdeij,"%3.0f",age );
+ /************** Inverse of matrix **************/
-     for(i=1; i<=nlstate;i++){
+ void ludcmp(double **a, int n, int *indx, double *d)
-       eip=0.;
+ {
-       vip=0.;
+   int i,imax,j,k;
-       for(j=1; j<=nlstate;j++){
+   double big,dum,sum,temp;
-         eip += eij[i][j][(int)age];
+   double *vv;
-         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];
+   vv=vector(1,n);
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+   *d=1.0;
-       }
+   for (i=1;i<=n;i++) {
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+     big=0.0;
-     }
+     for (j=1;j<=n;j++)
-     fprintf(ficresstdeij,"\n");
+       if ((temp=fabs(a[i][j])) > big) big=temp;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     fprintf(ficrescveij,"%3.0f",age );
+     vv[i]=1.0/big;
-     for(i=1; i<=nlstate;i++)
+   }
-       for(j=1; j<=nlstate;j++){
+   for (j=1;j<=n;j++) {
-         cptj= (j-1)*nlstate+i;
+     for (i=1;i<j;i++) {
-         for(i2=1; i2<=nlstate;i2++)
+       sum=a[i][j];
-           for(j2=1; j2<=nlstate;j2++){
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-             cptj2= (j2-1)*nlstate+i2;
+       a[i][j]=sum;
-             if(cptj2 <= cptj)
+     }
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+     big=0.0;
-           }
+     for (i=j;i<=n;i++) {
-       }
+       sum=a[i][j];
-     fprintf(ficrescveij,"\n");
+       for (k=1;k<j;k++)
+         sum -= a[i][k]*a[k][j];
-   }
+       a[i][j]=sum;
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+         big=dum;
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+         imax=i;
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+       }
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     }
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     if (j != imax) {
-   printf("\n");
+       for (k=1;k<=n;k++) {
-   fprintf(ficlog,"\n");
+         dum=a[imax][k];
+         a[imax][k]=a[j][k];
-   free_vector(xm,1,npar);
+         a[j][k]=dum;
-   free_vector(xp,1,npar);
+       }
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+       *d = -(*d);
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+       vv[imax]=vv[j];
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+     }
- }
+     indx[j]=imax;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
- /************ Variance ******************/
+     if (j != n) {
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+       dum=1.0/(a[j][j]);
- {
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   /* Variance of health expectancies */
+     }
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   }
-   /* double **newm;*/
+   free_vector(vv,1,n);  /* Doesn't work */
-   double **dnewm,**doldm;
+ ;
-   double **dnewmp,**doldmp;
+ }
-   int i, j, nhstepm, hstepm, h, nstepm ;
-   int k, cptcode;
+ void lubksb(double **a, int n, int *indx, double b[])
-   double *xp;
+ {
-   double **gp, **gm;  /* for var eij */
+   int i,ii=0,ip,j;
-   double ***gradg, ***trgradg; /*for var eij */
+   double sum;
-   double **gradgp, **trgradgp; /* for var p point j */
-   double *gpp, *gmp; /* for var p point j */
+   for (i=1;i<=n;i++) {
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+     ip=indx[i];
-   double ***p3mat;
+     sum=b[ip];
-   double age,agelim, hf;
+     b[ip]=b[i];
-   double ***mobaverage;
+     if (ii)
-   int theta;
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   char digit[4];
+     else if (sum) ii=i;
-   char digitp[25];
+     b[i]=sum;
+   }
-   char fileresprobmorprev[FILENAMELENGTH];
+   for (i=n;i>=1;i--) {
+     sum=b[i];
-   if(popbased==1){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-     if(mobilav!=0)
+     b[i]=sum/a[i][i];
-       strcpy(digitp,"-populbased-mobilav-");
+   }
-     else strcpy(digitp,"-populbased-nomobil-");
+ }
-   }
-   else
+ void pstamp(FILE *fichier)
-     strcpy(digitp,"-stablbased-");
+ {
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
-   if (mobilav!=0) {
+ }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+ /************ Frequencies ********************/
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ 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[])
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ {  /* Some frequencies */
-     }
-   }
+   int i, m, jk, j1, bool, z1,j;
+   int first;
-   strcpy(fileresprobmorprev,"prmorprev");
+   double ***freq; /* Frequencies */
-   sprintf(digit,"%-d",ij);
+   double *pp, **prop;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   char fileresp[FILENAMELENGTH];
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+   pp=vector(1,nlstate);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   strcpy(fileresp,"P_");
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   strcat(fileresp,fileresu);
-   }
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+     exit(0);
-   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);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   j1=0;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   j=cptcoveff;
-     for(i=1; i<=nlstate;i++)
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
+   first=1;
-   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficgp,"\n# Routine varevsij");
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
-   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");
+   /*    j1++; */
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
- /*   } */
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         scanf("%d", i);*/
-   pstamp(ficresvij);
+       for (i=-5; i<=nlstate+ndeath; i++)
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-   if(popbased==1)
+           for(m=iagemin; m <= iagemax+3; m++)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+             freq[i][jk][m]=0;
-   else
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+       for (i=1; i<=nlstate; i++)
-   fprintf(ficresvij,"# Age");
+         for(m=iagemin; m <= iagemax+3; m++)
-   for(i=1; i<=nlstate;i++)
+           prop[i][m]=0;
-     for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+       dateintsum=0;
-   fprintf(ficresvij,"\n");
+       k2cpt=0;
+       for (i=1; i<=imx; i++) {
-   xp=vector(1,npar);
+         bool=1;
-   dnewm=matrix(1,nlstate,1,npar);
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-   doldm=matrix(1,nlstate,1,nlstate);
+           for (z1=1; z1<=cptcoveff; z1++)
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               bool=0;
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
-   gpp=vector(nlstate+1,nlstate+ndeath);
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-   gmp=vector(nlstate+1,nlstate+ndeath);
+                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+             }
-   if(estepm < stepm){
+         }
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+         if (bool==1){
-   else  hstepm=estepm;
+           for(m=firstpass; m<=lastpass; m++){
-   /* For example we decided to compute the life expectancy with the smallest unit */
+             k2=anint[m][i]+(mint[m][i]/12.);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-      nhstepm is the number of hstepm from age to agelim
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-      nstepm is the number of stepm from age to agelin.
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-      Look at hpijx to understand the reason of that which relies in memory size
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-      and note for a fixed period like k years */
+               if (m<lastpass) {
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-      survival function given by stepm (the optimization length). Unfortunately it
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-      means that if the survival funtion is printed every two years of age and if
+               }
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-   */
+                 dateintsum=dateintsum+k2;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+                 k2cpt++;
-   agelim = AGESUP;
+               }
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+               /*}*/
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           }
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         }
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end i */
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-     gm=matrix(0,nhstepm,1,nlstate);
+       pstamp(ficresp);
+       if  (cptcovn>0) {
+         fprintf(ficresp, "\n#********** Variable ");
-     for(theta=1; theta <=npar; theta++){
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+         fprintf(ficresp, "**********\n#");
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         fprintf(ficlog, "\n#********** Variable ");
-       }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+         fprintf(ficlog, "**********\n#");
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
+       for(i=1; i<=nlstate;i++)
-       if (popbased==1) {
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-         if(mobilav ==0){
+       fprintf(ficresp, "\n");
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+       for(i=iagemin; i <= iagemax+3; i++){
-         }else{ /* mobilav */
+         if(i==iagemax+3){
-           for(i=1; i<=nlstate;i++)
+           fprintf(ficlog,"Total");
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }else{
-         }
+           if(first==1){
-       }
+             first=0;
+             printf("See log file for details...\n");
-       for(j=1; j<= nlstate; j++){
+           }
-         for(h=0; h<=nhstepm; h++){
+           fprintf(ficlog,"Age %d", i);
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+         }
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+         for(jk=1; jk <=nlstate ; jk++){
-         }
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-       }
+             pp[jk] += freq[jk][m][i];
-       /* This for computing probability of death (h=1 means
+         }
-          computed over hstepm matrices product = hstepm*stepm months)
+         for(jk=1; jk <=nlstate ; jk++){
-          as a weighted average of prlim.
+           for(m=-1, pos=0; m <=0 ; m++)
-       */
+             pos += freq[jk][m][i];
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+           if(pp[jk]>=1.e-10){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+             if(first==1){
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       }
+             }
-       /* end probability of death */
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+             if(first==1)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+           }
+         }
-       if (popbased==1) {
-         if(mobilav ==0){
+         for(jk=1; jk <=nlstate ; jk++){
-           for(i=1; i<=nlstate;i++)
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             prlim[i][i]=probs[(int)age][i][ij];
+             pp[jk] += freq[jk][m][i];
-         }else{ /* mobilav */
+         }
-           for(i=1; i<=nlstate;i++)
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+           pos += pp[jk];
-         }
+           posprop += prop[jk][i];
-       }
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-       for(j=1; j<= nlstate; j++){
+           if(pos>=1.e-5){
-         for(h=0; h<=nhstepm; h++){
+             if(first==1)
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-         }
+           }else{
-       }
+             if(first==1)
-       /* This for computing probability of death (h=1 means
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-          computed over hstepm matrices product = hstepm*stepm months)
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-          as a weighted average of prlim.
+           }
-       */
+           if( i <= iagemax){
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+             if(pos>=1.e-5){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-       }
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-       /* end probability of death */
+             }
+             else
-       for(j=1; j<= nlstate; j++) /* vareij */
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-         for(h=0; h<=nhstepm; h++){
+           }
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
-         }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+           for(m=-1; m <=nlstate+ndeath; m++)
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+             if(freq[jk][m][i] !=0 ) {
-       }
+             if(first==1)
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-     } /* End theta */
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+         if(i <= iagemax)
+           fprintf(ficresp,"\n");
-     for(h=0; h<=nhstepm; h++) /* veij */
+         if(first==1)
-       for(j=1; j<=nlstate;j++)
+           printf("Others in log...\n");
-         for(theta=1; theta <=npar; theta++)
+         fprintf(ficlog,"\n");
-           trgradg[h][j][theta]=gradg[h][theta][j];
+       }
+       /*}*/
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   }
-       for(theta=1; theta <=npar; theta++)
+   dateintmean=dateintsum/k2cpt;
-         trgradgp[j][theta]=gradgp[theta][j];
+   fclose(ficresp);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   free_vector(pp,1,nlstate);
-     for(i=1;i<=nlstate;i++)
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-       for(j=1;j<=nlstate;j++)
+   /* End of Freq */
-         vareij[i][j][(int)age] =0.;
+ }
-     for(h=0;h<=nhstepm;h++){
+ /************ Prevalence ********************/
-       for(k=0;k<=nhstepm;k++){
+ 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)
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+ {
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-         for(i=1;i<=nlstate;i++)
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-           for(j=1;j<=nlstate;j++)
+      We still use firstpass and lastpass as another selection.
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+   */
-       }
-     }
+   int i, m, jk, j1, bool, z1,j;
-     /* pptj */
+   double **prop;
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   double posprop;
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+   double  y2; /* in fractional years */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+   int iagemin, iagemax;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+   int first; /** to stop verbosity which is redirected to log file */
-         varppt[j][i]=doldmp[j][i];
-     /* end ppptj */
+   iagemin= (int) agemin;
-     /*  x centered again */
+   iagemax= (int) agemax;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   /*pp=vector(1,nlstate);*/
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-     if (popbased==1) {
+   j1=0;
-       if(mobilav ==0){
-         for(i=1; i<=nlstate;i++)
+   /*j=cptcoveff;*/
-           prlim[i][i]=probs[(int)age][i][ij];
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-       }else{ /* mobilav */
-         for(i=1; i<=nlstate;i++)
+   first=1;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-       }
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-     }
+       j1++;*/
-     /* This for computing probability of death (h=1 means
+       for (i=1; i<=nlstate; i++)
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+         for(m=iagemin; m <= iagemax+3; m++)
-        as a weighted average of prlim.
+           prop[i][m]=0.0;
-     */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for (i=1; i<=imx; i++) { /* Each individual */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+         bool=1;
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         if  (cptcovn>0) {
-     }
+           for (z1=1; z1<=cptcoveff; z1++)
-     /* end probability of death */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
+               bool=0;
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+         }
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+         if (bool==1) {
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-       for(i=1; i<=nlstate;i++){
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-       }
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-     }
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-     fprintf(ficresprobmorprev,"\n");
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-     fprintf(ficresvij,"%.0f ",age );
+                 /*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]]);*/
-     for(i=1; i<=nlstate;i++)
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-       for(j=1; j<=nlstate;j++){
+                 prop[s[m][i]][iagemax+3] += weight[i];
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+               }
-       }
+             }
-     fprintf(ficresvij,"\n");
+           } /* end selection of waves */
-     free_matrix(gp,0,nhstepm,1,nlstate);
+         }
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       }
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+       for(i=iagemin; i <= iagemax+3; i++){
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           posprop += prop[jk][i];
-   } /* End age */
+         }
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+         for(jk=1; jk <=nlstate ; jk++){
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+           if( i <=  iagemax){
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+             if(posprop>=1.e-5){
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+             } else{
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+               if(first==1){
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+                 first=0;
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+               }
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+             }
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+           }
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+         }/* end jk */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+       }/* end 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);
+     /*} *//* end i1 */
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   } /* end j1 */
- */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   free_vector(xp,1,npar);
+ }  /* End of prevalence */
-   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
+ /************* Waves Concatenation ***************/
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+ 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)
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ {
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   fclose(ficresprobmorprev);
+      Death is a valid wave (if date is known).
-   fflush(ficgp);
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-   fflush(fichtm);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
- }  /* end varevsij */
+      and mw[mi+1][i]. dh depends on stepm.
+      */
- /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+   int i, mi, m;
- {
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   /* Variance of prevalence limit */
+      double sum=0., jmean=0.;*/
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   int first;
-   double **newm;
+   int j, k=0,jk, ju, jl;
-   double **dnewm,**doldm;
+   double sum=0.;
-   int i, j, nhstepm, hstepm;
+   first=0;
-   int k, cptcode;
+   jmin=100000;
-   double *xp;
+   jmax=-1;
-   double *gp, *gm;
+   jmean=0.;
-   double **gradg, **trgradg;
+   for(i=1; i<=imx; i++){
-   double age,agelim;
+     mi=0;
-   int theta;
+     m=firstpass;
+     while(s[m][i] <= nlstate){
-   pstamp(ficresvpl);
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+         mw[++mi][i]=m;
-   fprintf(ficresvpl,"# Age");
+       if(m >=lastpass)
-   for(i=1; i<=nlstate;i++)
+         break;
-       fprintf(ficresvpl," %1d-%1d",i,i);
+       else
-   fprintf(ficresvpl,"\n");
+         m++;
+     }/* end while */
-   xp=vector(1,npar);
+     if (s[m][i] > nlstate){
-   dnewm=matrix(1,nlstate,1,npar);
+       mi++;     /* Death is another wave */
-   doldm=matrix(1,nlstate,1,nlstate);
+       /* if(mi==0)  never been interviewed correctly before death */
+          /* Only death is a correct wave */
-   hstepm=1*YEARM; /* Every year of age */
+       mw[mi][i]=m;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     }
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     wav[i]=mi;
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     if(mi==0){
-     if (stepm >= YEARM) hstepm=1;
+       nbwarn++;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       if(first==0){
-     gradg=matrix(1,npar,1,nlstate);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-     gp=vector(1,nlstate);
+         first=1;
-     gm=vector(1,nlstate);
+       }
+       if(first==1){
-     for(theta=1; theta <=npar; theta++){
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+       }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     } /* end mi==0 */
-       }
+   } /* End individuals */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       for(i=1;i<=nlstate;i++)
+   for(i=1; i<=imx; i++){
-         gp[i] = prlim[i][i];
+     for(mi=1; mi<wav[i];mi++){
+       if (stepm <=0)
-       for(i=1; i<=npar; i++) /* Computes gradient */
+         dh[mi][i]=1;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       else{
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-       for(i=1;i<=nlstate;i++)
+           if (agedc[i] < 2*AGESUP) {
-         gm[i] = prlim[i][i];
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-       for(i=1;i<=nlstate;i++)
+             else if(j<0){
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+               nberr++;
-     } /* End theta */
+               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 */
-     trgradg =matrix(1,nlstate,1,npar);
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-     for(j=1; j<=nlstate;j++)
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-       for(theta=1; theta <=npar; theta++)
+             }
-         trgradg[j][theta]=gradg[theta][j];
+             k=k+1;
+             if (j >= jmax){
-     for(i=1;i<=nlstate;i++)
+               jmax=j;
-       varpl[i][(int)age] =0.;
+               ijmax=i;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+             }
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+             if (j <= jmin){
-     for(i=1;i<=nlstate;i++)
+               jmin=j;
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+               ijmin=i;
+             }
-     fprintf(ficresvpl,"%.0f ",age );
+             sum=sum+j;
-     for(i=1; i<=nlstate;i++)
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-     fprintf(ficresvpl,"\n");
+           }
-     free_vector(gp,1,nlstate);
+         }
-     free_vector(gm,1,nlstate);
+         else{
-     free_matrix(gradg,1,npar,1,nlstate);
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-     free_matrix(trgradg,1,nlstate,1,npar);
+ /*        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]); */
-   } /* End age */
+           k=k+1;
-   free_vector(xp,1,npar);
+           if (j >= jmax) {
-   free_matrix(doldm,1,nlstate,1,npar);
+             jmax=j;
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+             ijmax=i;
+           }
- }
+           else if (j <= jmin){
+             jmin=j;
- /************ Variance of one-step probabilities  ******************/
+             ijmin=i;
- 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[])
+           }
- {
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-   int i, j=0,  i1, k1, l1, t, tj;
+           /*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]);*/
-   int k2, l2, j1,  z1;
+           if(j<0){
-   int k=0,l, cptcode;
+             nberr++;
-   int first=1, first1;
+             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]);
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   double **dnewm,**doldm;
+           }
-   double *xp;
+           sum=sum+j;
-   double *gp, *gm;
+         }
-   double **gradg, **trgradg;
+         jk= j/stepm;
-   double **mu;
+         jl= j -jk*stepm;
-   double age,agelim, cov[NCOVMAX];
+         ju= j -(jk+1)*stepm;
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-   int theta;
+           if(jl==0){
-   char fileresprob[FILENAMELENGTH];
+             dh[mi][i]=jk;
-   char fileresprobcov[FILENAMELENGTH];
+             bh[mi][i]=0;
-   char fileresprobcor[FILENAMELENGTH];
+           }else{ /* We want a negative bias in order to only have interpolation ie
+                   * to avoid the price of an extra matrix product in likelihood */
-   double ***varpij;
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
-   strcpy(fileresprob,"prob");
+           }
-   strcat(fileresprob,fileres);
+         }else{
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+           if(jl <= -ju){
-     printf("Problem with resultfile: %s\n", fileresprob);
+             dh[mi][i]=jk;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+             bh[mi][i]=jl;       /* bias is positive if real duration
-   }
+                                  * is higher than the multiple of stepm and negative otherwise.
-   strcpy(fileresprobcov,"probcov");
+                                  */
-   strcat(fileresprobcov,fileres);
+           }
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+           else{
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+             dh[mi][i]=jk+1;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+             bh[mi][i]=ju;
-   }
+           }
-   strcpy(fileresprobcor,"probcor");
+           if(dh[mi][i]==0){
-   strcat(fileresprobcor,fileres);
+             dh[mi][i]=1; /* At least one step */
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+             bh[mi][i]=ju; /* At least one step */
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+           }
-   }
+         } /* end if mle */
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+       }
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+     } /* end wave */
-   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);
+   jmean=sum/k;
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   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);
-   pstamp(ficresprob);
+  }
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   fprintf(ficresprob,"# Age");
+ /*********** Tricode ****************************/
-   pstamp(ficresprobcov);
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+ {
-   fprintf(ficresprobcov,"# Age");
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   pstamp(ficresprobcor);
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-   fprintf(ficresprobcor,"# Age");
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+    * nbcode[Tvar[j]][1]=
+   */
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   int modmaxcovj=0; /* Modality max of covariates j */
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   int cptcode=0; /* Modality max of covariates j */
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   int modmincovj=0; /* Modality min of covariates j */
-     }
-  /* fprintf(ficresprob,"\n");
-   fprintf(ficresprobcov,"\n");
+   cptcoveff=0;
-   fprintf(ficresprobcor,"\n");
-  */
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-  xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   /* Loop on covariates without age and products */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
-   first=1;
+                                modality of this covariate Vj*/
-   fprintf(ficgp,"\n# Routine varprob");
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+                                     * If product of Vn*Vm, still boolean *:
-   fprintf(fichtm,"\n");
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+                                       modality of the nth covariate of individual i. */
-   file %s<br>\n",optionfilehtmcov);
+       if (ij > modmaxcovj)
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+         modmaxcovj=ij;
- and drawn. It helps understanding how is the covariance between two incidences.\
+       else if (ij < modmincovj)
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+         modmincovj=ij;
-   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 ((ij < -1) && (ij > NCOVMAX)){
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+         exit(1);
- standard deviations wide on each axis. <br>\
+       }else
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+       /*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
-   cov[1]=1;
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   tj=cptcoveff;
+          female is 1, then modmaxcovj=1.*/
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     } /* end for loop on individuals i */
-   j1=0;
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   for(t=1; t<=tj;t++){
+     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-     for(i1=1; i1<=ncodemax[t];i1++){
+     cptcode=modmaxcovj;
-       j1++;
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-       if  (cptcovn>0) {
+    /*for (i=0; i<=cptcode; i++) {*/
-         fprintf(ficresprob, "\n#********** Variable ");
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-         fprintf(ficresprob, "**********\n#\n");
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         if( k != -1){
-         fprintf(ficresprobcov, "**********\n#\n");
+           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered excluding
-         fprintf(ficgp, "\n#********** Variable ");
+                              undefined. Usually 2: 0 and 1. */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         }
-         fprintf(ficgp, "**********\n#\n");
+         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+       }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
-         fprintf(ficresprobcor, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-         fprintf(ficresprobcor, "**********\n#");
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-       }
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
+        modmincovj=3; modmaxcovj = 7;
-       for (age=bage; age<=fage; age ++){
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-         cov[2]=age;
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-         for (k=1; k<=cptcovn;k++) {
+        defining two dummy variables: variables V1_1 and V1_2.
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+        nbcode[Tvar[j]][ij]=k;
-         }
+        nbcode[Tvar[j]][1]=0;
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+        nbcode[Tvar[j]][2]=1;
-         for (k=1; k<=cptcovprod;k++)
+        nbcode[Tvar[j]][3]=2;
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+        To be continued (not working yet).
+     */
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+     ij=0; /* ij is similar to i but can jump over null modalities */
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+           break;
+         }
-         for(theta=1; theta <=npar; theta++){
+         ij++;
-           for(i=1; i<=npar; i++)
+         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+         cptcode = ij; /* New max modality for covar j */
+     } /* end of loop on modality i=-1 to 1 or more */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-           k=0;
+     /*  /\*recode from 0 *\/ */
-           for(i=1; i<= (nlstate); i++){
+     /*                               k is a modality. If we have model=V1+V1*sex  */
-             for(j=1; j<=(nlstate+ndeath);j++){
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-               k=k+1;
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-               gp[k]=pmmij[i][j];
+     /*  } */
-             }
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-           }
+     /*  if (ij > ncodemax[j]) { */
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-           for(i=1; i<=npar; i++)
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+     /*    break; */
+     /*  } */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     /*   }  /\* end of loop on modality k *\/ */
-           k=0;
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-           for(i=1; i<=(nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-               k=k+1;
-               gm[k]=pmmij[i][j];
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-             }
+    /* 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 */
+    Ndum[ij]++; /* Might be supersed V1 + V1*age */
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+  }
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-         }
+  ij=0;
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-           for(theta=1; theta <=npar; theta++)
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-             trgradg[j][theta]=gradg[theta][j];
+      ij++;
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+      Tvaraff[ij]=i; /*For printing (unclear) */
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+    }else{
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+        /* Tvaraff[ij]=0; */
-         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);
+  /* ij--; */
+  cptcoveff=ij; /*Number of total covariates*/
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+ }
-         k=0;
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
+ /*********** Health Expectancies ****************/
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-           }
-         }
+ {
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   /* Health expectancies, no variances */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   int i, j, nhstepm, hstepm, h, nstepm;
-             varpij[i][j][(int)age] = doldm[i][j];
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
-         /*printf("\n%d ",(int)age);
+   double ***p3mat;
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+   double eip;
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   pstamp(ficreseij);
-           }*/
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   fprintf(ficreseij,"# Age");
-         fprintf(ficresprob,"\n%d ",(int)age);
+   for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+     for(j=1; j<=nlstate;j++){
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+     fprintf(ficreseij," e%1d. ",i);
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+   }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+   fprintf(ficreseij,"\n");
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
+   if(estepm < stepm){
-         i=0;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         for (k=1; k<=(nlstate);k++){
+   }
-           for (l=1; l<=(nlstate+ndeath);l++){
+   else  hstepm=estepm;
-             i=i++;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+    * This is mainly to measure the difference between two models: for example
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-             for (j=1; j<=i;j++){
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+    * progression in between and thus overestimating or underestimating according
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+    * 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
-         }/* end of loop for state */
+    * hypothesis. A more precise result, taking into account a more precise
-       } /* end of loop for age */
+    * curvature will be obtained if estepm is as small as stepm. */
-       /* Confidence intervalle of pij  */
+   /* 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.
-         fprintf(ficgp,"\nset noparametric;unset label");
+      nhstepm is the number of hstepm from age to agelim
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+      nstepm is the number of stepm from age to agelin.
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+      Look at hpijx to understand the reason of that which relies in memory size
-         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);
+      and note for a fixed period like estepm months */
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+      survival function given by stepm (the optimization length). Unfortunately it
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      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
+      results. So we changed our mind and took the option of the best precision.
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+   */
-       first1=1;
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+   agelim=AGESUP;
-           if(l2==k2) continue;
+   /* If stepm=6 months */
-           j=(k2-1)*(nlstate+ndeath)+l2;
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-           for (k1=1; k1<=(nlstate);k1++){
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
+ /* nhstepm age range expressed in number of stepm */
-               i=(k1-1)*(nlstate+ndeath)+l1;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-               if(i<=j) continue;
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-               for (age=bage; age<=fage; age ++){
+   /* if (stepm >= YEARM) hstepm=1;*/
-                 if ((int)age %5==0){
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   for (age=bage; age<=fage; age ++){
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-                   c12=cv12/sqrt(v1*v2);
+     /* if (stepm >= YEARM) hstepm=1;*/
-                   /* Computing eigen value of matrix of covariance */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     /* If stepm=6 months */
-                   /* Eigen vectors */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-                   /*v21=sqrt(1.-v11*v11); *//* error */
-                   v21=(lc1-v1)/cv12*v11;
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-                   v12=-v21;
-                   v22=v11;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-                   tnalp=v21/v11;
-                   if(first1==1){
+     printf("%d|",(int)age);fflush(stdout);
-                     first1=0;
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-                     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);
-                   }
+     /* Computing expectancies */
-                   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);
+     for(i=1; i<=nlstate;i++)
-                   /*printf(fignu*/
+       for(j=1; j<=nlstate;j++)
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-                   if(first==1){
-                     first=0;
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-                     fprintf(ficgp,"\nset parametric;unset label");
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+         }
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+     fprintf(ficreseij,"%3.0f",age );
-  :<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,\
+       eip=0;
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+       for(j=1; j<=nlstate;j++){
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         eip +=eij[i][j][(int)age];
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-                     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(ficreseij,"%9.4f", eip );
-                     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(ficreseij,"\n");
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   }
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                   }else{
+   printf("\n");
-                     first=0;
+   fprintf(ficlog,"\n");
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ }
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                     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",\
+ 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[] )
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ {
-                   }/* if first */
+   /* Covariances of health expectancies eij and of total life expectancies according
-                 } /* age mod 5 */
+    to initial status i, ei. .
-               } /* end loop age */
+   */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-               first=1;
+   int nhstepma, nstepma; /* Decreasing with age */
-             } /*l12 */
+   double age, agelim, hf;
-           } /* k12 */
+   double ***p3matp, ***p3matm, ***varhe;
-         } /*l1 */
+   double **dnewm,**doldm;
-       }/* k1 */
+   double *xp, *xm;
-     } /* loop covariates */
+   double **gp, **gm;
-   }
+   double ***gradg, ***trgradg;
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   int theta;
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   double eip, vip;
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_vector(xp,1,npar);
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   fclose(ficresprob);
+   xp=vector(1,npar);
-   fclose(ficresprobcov);
+   xm=vector(1,npar);
-   fclose(ficresprobcor);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   fflush(ficgp);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   fflush(fichtmcov);
- }
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   fprintf(ficresstdeij,"# Age");
- /******************* Printing html file ***********/
+   for(i=1; i<=nlstate;i++){
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+     for(j=1; j<=nlstate;j++)
-                   int lastpass, int stepm, int weightopt, char model[],\
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     fprintf(ficresstdeij," e%1d. ",i);
-                   int popforecast, int estepm ,\
+   }
-                   double jprev1, double mprev1,double anprev1, \
+   fprintf(ficresstdeij,"\n");
-                   double jprev2, double mprev2,double anprev2){
-   int jj1, k1, i1, cpt;
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   fprintf(ficrescveij,"# Age");
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   for(i=1; i<=nlstate;i++)
- </ul>");
+     for(j=1; j<=nlstate;j++){
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+       cptj= (j-1)*nlstate+i;
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+       for(i2=1; i2<=nlstate;i2++)
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+         for(j2=1; j2<=nlstate;j2++){
-    fprintf(fichtm,"\
+           cptj2= (j2-1)*nlstate+i2;
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+           if(cptj2 <= cptj)
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-    fprintf(fichtm,"\
+         }
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+     }
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   fprintf(ficrescveij,"\n");
-    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(estepm < stepm){
-    <a href=\"%s\">%s</a> <br>\n",
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+   }
-    fprintf(fichtm,"\
+   else  hstepm=estepm;
-  - Population projections by age and states: \
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+    * 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
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
-  m=cptcoveff;
+    * to the curvature of the survival function. If, for the same date, we
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
-  jj1=0;
+    * hypothesis. A more precise result, taking into account a more precise
-  for(k1=1; k1<=m;k1++){
+    * curvature will be obtained if estepm is as small as stepm. */
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      jj1++;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-      if (cptcovn > 0) {
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+      nhstepm is the number of hstepm from age to agelim
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+      nstepm is the number of stepm from age to agelin.
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+      Look at hpijx to understand the reason of that which relies in memory size
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      and note for a fixed period like estepm months */
-      }
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-      /* Pij */
+      survival function given by stepm (the optimization length). Unfortunately it
-      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> \
+      means that if the survival funtion is printed only each two years of age and if
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      /* Quasi-incidences */
+      results. So we changed our mind and took the option of the best precision.
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+   */
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        /* Period (stable) prevalence in each health state */
+   /* If stepm=6 months */
-        for(cpt=1; cpt<nlstate;cpt++){
+   /* nhstepm age range expressed in number of stepm */
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+   agelim=AGESUP;
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-        }
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   /* if (stepm >= YEARM) hstepm=1;*/
-         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> \
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-      }
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-    } /* end i1 */
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  }/* End k1 */
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-  fprintf(fichtm,"</ul>");
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-  fprintf(fichtm,"\
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   for (age=bage; age<=fage; age ++){
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     /* if (stepm >= YEARM) hstepm=1;*/
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-  fprintf(fichtm,"\
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     /* If stepm=6 months */
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-  fprintf(fichtm,"\
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-  fprintf(fichtm,"\
+     /* Computing  Variances of health expectancies */
-  - 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): \
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-    <a href=\"%s\">%s</a> <br>\n</li>",
+        decrease memory allocation */
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+     for(theta=1; theta <=npar; theta++){
-  fprintf(fichtm,"\
+       for(i=1; i<=npar; i++){
-  - (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): \
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+       }
-  fprintf(fichtm,"\
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-  - 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",
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-  fprintf(fichtm,"\
+       for(j=1; j<= nlstate; j++){
-  - 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",
+         for(i=1; i<=nlstate; i++){
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+           for(h=0; h<=nhstepm-1; h++){
-  fprintf(fichtm,"\
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+           }
+         }
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+       }
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+       for(ij=1; ij<= nlstate*nlstate; ij++)
- /*      <br>",fileres,fileres,fileres,fileres); */
+         for(h=0; h<=nhstepm-1; h++){
- /*  else  */
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+         }
-  fflush(fichtm);
+     }/* End theta */
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+     for(h=0; h<=nhstepm-1; h++)
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       for(j=1; j<=nlstate*nlstate;j++)
+         for(theta=1; theta <=npar; theta++)
-  jj1=0;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      jj1++;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-      if (cptcovn > 0) {
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         varhe[ij][ji][(int)age] =0.;
-        for (cpt=1; cpt<=cptcoveff;cpt++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+      printf("%d|",(int)age);fflush(stdout);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      }
+      for(h=0;h<=nhstepm-1;h++){
-      for(cpt=1; cpt<=nlstate;cpt++) {
+       for(k=0;k<=nhstepm-1;k++){
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-      }
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
- health expectancies in states (1) and (2): %s%d.png<br>\
+       }
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+     }
-    } /* end i1 */
-  }/* End k1 */
+     /* Computing expectancies */
-  fprintf(fichtm,"</ul>");
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-  fflush(fichtm);
+     for(i=1; i<=nlstate;i++)
- }
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- /******************* Gnuplot file **************/
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+           /* 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]);*/
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+         }
-   int ng;
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+     fprintf(ficresstdeij,"%3.0f",age );
- /*     printf("Problem with file %s",optionfilegnuplot); */
+     for(i=1; i<=nlstate;i++){
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+       eip=0.;
- /*   } */
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
-   /*#ifdef windows */
+         eip += eij[i][j][(int)age];
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-     /*#endif */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-   m=pow(2,cptcoveff);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
-   strcpy(dirfileres,optionfilefiname);
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   strcpy(optfileres,"vpl");
+     }
-  /* 1eme*/
+     fprintf(ficresstdeij,"\n");
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
-    for (k1=1; k1<= m ; k1 ++) {
+     fprintf(ficrescveij,"%3.0f",age );
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+     for(i=1; i<=nlstate;i++)
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+       for(j=1; j<=nlstate;j++){
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+         cptj= (j-1)*nlstate+i;
- set ylabel \"Probability\" \n\
+         for(i2=1; i2<=nlstate;i2++)
- set ter png small\n\
+           for(j2=1; j2<=nlstate;j2++){
- set size 0.65,0.65\n\
+             cptj2= (j2-1)*nlstate+i2;
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-      for (i=1; i<= nlstate ; i ++) {
+           }
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       }
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+     fprintf(ficrescveij,"\n");
-      }
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+   }
-      for (i=1; i<= nlstate ; i ++) {
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-      }
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-      for (i=1; i<= nlstate ; i ++) {
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   printf("\n");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   fprintf(ficlog,"\n");
-      }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+   free_vector(xm,1,npar);
-    }
+   free_vector(xp,1,npar);
-   }
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   /*2 eme*/
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-   for (k1=1; k1<= m ; k1 ++) {
+ }
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+ /************ Variance ******************/
+  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
-     for (i=1; i<= nlstate+1 ; i ++) {
+ {
-       k=2*i;
+   /* Variance of health expectancies */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-       for (j=1; j<= nlstate+1 ; j ++) {
+   /* double **newm;*/
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+   int movingaverage();
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+   double **dnewm,**doldm;
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+   double **dnewmp,**doldmp;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   int i, j, nhstepm, hstepm, h, nstepm ;
-       for (j=1; j<= nlstate+1 ; j ++) {
+   int k;
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   double *xp;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   double **gp, **gm;  /* for var eij */
-       }
+   double ***gradg, ***trgradg; /*for var eij */
-       fprintf(ficgp,"\" t\"\" w l 0,");
+   double **gradgp, **trgradgp; /* for var p point j */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   double *gpp, *gmp; /* for var p point j */
-       for (j=1; j<= nlstate+1 ; j ++) {
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   double ***p3mat;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   double age,agelim, hf;
-       }
+   double ***mobaverage;
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+   int theta;
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+   char digit[4];
-     }
+   char digitp[25];
-   }
+   char fileresprobmorprev[FILENAMELENGTH];
-   /*3eme*/
+   if(popbased==1){
-   for (k1=1; k1<= m ; k1 ++) {
+     if(mobilav!=0)
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       strcpy(digitp,"-POPULBASED-MOBILAV_");
-       /*       k=2+nlstate*(2*cpt-2); */
+     else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-       k=2+(nlstate+1)*(cpt-1);
+   }
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+   else
-       fprintf(ficgp,"set ter png small\n\
+     strcpy(digitp,"-STABLBASED_");
- set size 0.65,0.65\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+   if (mobilav!=0) {
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+     }
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   }
-       */
+   strcpy(fileresprobmorprev,"PRMORPREV-");
-       for (i=1; i< nlstate ; i ++) {
+   sprintf(digit,"%-d",ij);
-         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);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-         /*      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);*/
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-       }
+   strcat(fileresprobmorprev,fileresu);
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     }
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   }
-   /* CV preval stable (period) */
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-       k=3;
+   pstamp(ficresprobmorprev);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+   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(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
- set ter png small\nset size 0.65,0.65\n\
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- unset log y\n\
+     fprintf(ficresprobmorprev," p.%-d SE",j);
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-       for (i=1; i< nlstate ; i ++)
+   }
-         fprintf(ficgp,"+$%d",k+i+1);
+   fprintf(ficresprobmorprev,"\n");
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+   fprintf(ficgp,"\n# Routine varevsij");
+   fprintf(ficgp,"\nunset title \n");
-       l=3+(nlstate+ndeath)*cpt;
+ /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-       for (i=1; i< nlstate ; i ++) {
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-         l=3+(nlstate+ndeath)*cpt;
+ /*   } */
-         fprintf(ficgp,"+$%d",l+i+1);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       }
+   pstamp(ficresvij);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-     }
+   if(popbased==1)
-   }
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+   else
-   /* proba elementaires */
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   for(i=1,jk=1; i <=nlstate; i++){
+   fprintf(ficresvij,"# Age");
-     for(k=1; k <=(nlstate+ndeath); k++){
+   for(i=1; i<=nlstate;i++)
-       if (k != i) {
+     for(j=1; j<=nlstate;j++)
-         for(j=1; j <=ncovmodel; j++){
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+   fprintf(ficresvij,"\n");
-           jk++;
-           fprintf(ficgp,"\n");
+   xp=vector(1,npar);
-         }
+   dnewm=matrix(1,nlstate,1,npar);
-       }
+   doldm=matrix(1,nlstate,1,nlstate);
-     }
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-    }
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-      for(jk=1; jk <=m; jk++) {
+   gpp=vector(nlstate+1,nlstate+ndeath);
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-        if (ng==2)
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-        else
+   if(estepm < stepm){
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+   }
-        i=1;
+   else  hstepm=estepm;
-        for(k2=1; k2<=nlstate; k2++) {
+   /* For example we decided to compute the life expectancy with the smallest unit */
-          k3=i;
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-          for(k=1; k<=(nlstate+ndeath); k++) {
+      nhstepm is the number of hstepm from age to agelim
-            if (k != k2){
+      nstepm is the number of stepm from age to agelin.
-              if(ng==2)
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-              else
+      survival function given by stepm (the optimization length). Unfortunately it
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+      means that if the survival funtion is printed every two years of age and if
-              ij=1;
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-              for(j=3; j <=ncovmodel; j++) {
+      results. So we changed our mind and took the option of the best precision.
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+   */
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-                  ij++;
+   agelim = AGESUP;
-                }
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-                else
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-              }
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-              fprintf(ficgp,")/(1");
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+     gp=matrix(0,nhstepm,1,nlstate);
-              for(k1=1; k1 <=nlstate; k1++){
+     gm=matrix(0,nhstepm,1,nlstate);
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-                ij=1;
-                for(j=3; j <=ncovmodel; j++){
+     for(theta=1; theta <=npar; theta++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-                    ij++;
+       }
-                  }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-                  else
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-                }
+       if (popbased==1) {
-                fprintf(ficgp,")");
+         if(mobilav ==0){
-              }
+           for(i=1; i<=nlstate;i++)
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+             prlim[i][i]=probs[(int)age][i][ij];
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+         }else{ /* mobilav */
-              i=i+ncovmodel;
+           for(i=1; i<=nlstate;i++)
-            }
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-          } /* end k */
+         }
-        } /* end k2 */
+       }
-      } /* end jk */
-    } /* end ng */
+       for(j=1; j<= nlstate; j++){
-    fflush(ficgp);
+         for(h=0; h<=nhstepm; h++){
- }  /* end gnuplot */
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+         }
- /*************** Moving average **************/
+       }
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-   int i, cpt, cptcod;
+          as a weighted average of prlim.
-   int modcovmax =1;
+       */
-   int mobilavrange, mob;
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   double age;
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+       }
-                            a covariate has 2 modalities */
+       /* end probability of death */
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     if(mobilav==1) mobilavrange=5; /* default */
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-     else mobilavrange=mobilav;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
-     for (age=bage; age<=fage; age++)
-       for (i=1; i<=nlstate;i++)
+       if (popbased==1) {
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+         if(mobilav ==0){
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+           for(i=1; i<=nlstate;i++)
-     /* We keep the original values on the extreme ages bage, fage and for
+             prlim[i][i]=probs[(int)age][i][ij];
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         }else{ /* mobilav */
-        we use a 5 terms etc. until the borders are no more concerned.
+           for(i=1; i<=nlstate;i++)
-     */
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+         }
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+       }
-         for (i=1; i<=nlstate;i++){
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+         for(h=0; h<=nhstepm; h++){
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+         }
-               }
+       }
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+       /* This for computing probability of death (h=1 means
-           }
+          computed over hstepm matrices product = hstepm*stepm months)
-         }
+          as a weighted average of prlim.
-       }/* end age */
+       */
-     }/* end mob */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   }else return -1;
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-   return 0;
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
- }/* End movingaverage */
+       }
+       /* end probability of death */
- /************** Forecasting ******************/
+       for(j=1; j<= nlstate; j++) /* vareij */
- 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(h=0; h<=nhstepm; h++){
-   /* proj1, year, month, day of starting projection
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-      agemin, agemax range of age
+         }
-      dateprev1 dateprev2 range of dates during which prevalence is computed
-      anproj2 year of en of projection (same day and month as proj1).
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-   */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+       }
-   int *popage;
-   double agec; /* generic age */
+     } /* End theta */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-   double *popeffectif,*popcount;
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   double ***p3mat;
-   double ***mobaverage;
+     for(h=0; h<=nhstepm; h++) /* veij */
-   char fileresf[FILENAMELENGTH];
+       for(j=1; j<=nlstate;j++)
+         for(theta=1; theta <=npar; theta++)
-   agelim=AGESUP;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-   strcpy(fileresf,"f");
+       for(theta=1; theta <=npar; theta++)
-   strcat(fileresf,fileres);
+         trgradgp[j][theta]=gradgp[theta][j];
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     printf("Problem with forecast resultfile: %s\n", fileresf);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   }
+     for(i=1;i<=nlstate;i++)
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+       for(j=1;j<=nlstate;j++)
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+         vareij[i][j][(int)age] =0.;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+     for(h=0;h<=nhstepm;h++){
+       for(k=0;k<=nhstepm;k++){
-   if (mobilav!=0) {
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+         for(i=1;i<=nlstate;i++)
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           for(j=1;j<=nlstate;j++)
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-     }
+       }
-   }
+     }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /* pptj */
-   if (stepm<=12) stepsize=1;
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-   if(estepm < stepm){
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-   }
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-   else  hstepm=estepm;
+         varppt[j][i]=doldmp[j][i];
+     /* end ppptj */
-   hstepm=hstepm/stepm;
+     /*  x centered again */
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-                                fractional in yp1 */
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
-   anprojmean=yp;
-   yp2=modf((yp1*12),&yp);
+     if (popbased==1) {
-   mprojmean=yp;
+       if(mobilav ==0){
-   yp1=modf((yp2*30.5),&yp);
+         for(i=1; i<=nlstate;i++)
-   jprojmean=yp;
+           prlim[i][i]=probs[(int)age][i][ij];
-   if(jprojmean==0) jprojmean=1;
+       }else{ /* mobilav */
-   if(mprojmean==0) jprojmean=1;
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-   i1=cptcoveff;
+       }
-   if (cptcovn < 1){i1=1;}
+     }
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+     /* This for computing probability of death (h=1 means
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+        as a weighted average of prlim.
+     */
- /*            if (h==(int)(YEARM*yearp)){ */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       k=k+1;
+     }
-       fprintf(ficresf,"\n#******");
+     /* end probability of death */
-       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]]);
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-       }
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresf,"******\n");
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+       for(i=1; i<=nlstate;i++){
-       for(j=1; j<=nlstate+ndeath;j++){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-         for(i=1; i<=nlstate;i++)
+       }
-           fprintf(ficresf," p%d%d",i,j);
+     }
-         fprintf(ficresf," p.%d",j);
+     fprintf(ficresprobmorprev,"\n");
-       }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+     fprintf(ficresvij,"%.0f ",age );
-         fprintf(ficresf,"\n");
+     for(i=1; i<=nlstate;i++)
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       for(j=1; j<=nlstate;j++){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+       }
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+     fprintf(ficresvij,"\n");
-           nhstepm = nhstepm/hstepm;
+     free_matrix(gp,0,nhstepm,1,nlstate);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     free_matrix(gm,0,nhstepm,1,nlstate);
-           oldm=oldms;savm=savms;
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           for (h=0; h<=nhstepm; h++){
+   } /* End age */
-             if (h*hstepm/YEARM*stepm ==yearp) {
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-               fprintf(ficresf,"\n");
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-               for(j=1;j<=cptcoveff;j++)
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+   /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-             }
+   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
-             for(j=1; j<=nlstate+ndeath;j++) {
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-               ppij=0.;
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-               for(i=1; i<=nlstate;i++) {
+   fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-                 if (mobilav==1)
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+ /*   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); */
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                 }
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                 if (h*hstepm/YEARM*stepm== yearp) {
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-                 }
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-               } /* end i */
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
-               if (h*hstepm/YEARM*stepm==yearp) {
+ */
-                 fprintf(ficresf," %.3f", ppij);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-               }
+   fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-             }/* end j */
-           } /* end h */
+   free_vector(xp,1,npar);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-         } /* end agec */
+   free_matrix(dnewm,1,nlstate,1,npar);
-       } /* end yearp */
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     } /* end cptcod */
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   } /* end  cptcov */
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprobmorprev);
+   fflush(ficgp);
-   fclose(ficresf);
+   fflush(fichtm);
- }
+ }  /* end varevsij */
- /************** Forecasting *****not tested NB*************/
+ /************ Variance of prevlim ******************/
- 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){
+  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 *ncvyear, int ij, char strstart[])
+ {
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
-   int *popage;
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
+   double **dnewm,**doldm;
-   double ***p3mat,***tabpop,***tabpopprev;
+   int i, j, nhstepm, hstepm;
-   double ***mobaverage;
+   double *xp;
-   char filerespop[FILENAMELENGTH];
+   double *gp, *gm;
+   double **gradg, **trgradg;
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double age,agelim;
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   int theta;
-   agelim=AGESUP;
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   pstamp(ficresvpl);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   fprintf(ficresvpl,"# Age");
+   for(i=1; i<=nlstate;i++)
+       fprintf(ficresvpl," %1d-%1d",i,i);
-   strcpy(filerespop,"pop");
+   fprintf(ficresvpl,"\n");
-   strcat(filerespop,fileres);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+   xp=vector(1,npar);
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+   dnewm=matrix(1,nlstate,1,npar);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   doldm=matrix(1,nlstate,1,nlstate);
-   }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   hstepm=1*YEARM; /* Every year of age */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGESUP;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   if (mobilav!=0) {
+     if (stepm >= YEARM) hstepm=1;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+     gradg=matrix(1,npar,1,nlstate);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     gp=vector(1,nlstate);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     gm=vector(1,nlstate);
-     }
-   }
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   if (stepm<=12) stepsize=1;
+       }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
-   agelim=AGESUP;
+       for(i=1;i<=nlstate;i++)
+         gp[i] = prlim[i][i];
-   hstepm=1;
-   hstepm=hstepm/stepm;
+       for(i=1; i<=npar; i++) /* Computes gradient */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   if (popforecast==1) {
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+       for(i=1;i<=nlstate;i++)
-       printf("Problem with population file : %s\n",popfile);exit(0);
+         gm[i] = prlim[i][i];
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-     }
+       for(i=1;i<=nlstate;i++)
-     popage=ivector(0,AGESUP);
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-     popeffectif=vector(0,AGESUP);
+     } /* End theta */
-     popcount=vector(0,AGESUP);
+     trgradg =matrix(1,nlstate,1,npar);
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     for(j=1; j<=nlstate;j++)
+       for(theta=1; theta <=npar; theta++)
-     imx=i;
+         trgradg[j][theta]=gradg[theta][j];
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
+     for(i=1;i<=nlstate;i++)
+       varpl[i][(int)age] =0.;
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+     if((int)age==67 ||(int)age== 66 ){
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-       k=k+1;
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-       fprintf(ficrespop,"\n#******");
+     }else{
-       for(j=1;j<=cptcoveff;j++) {
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-       }
+     }
-       fprintf(ficrespop,"******\n");
+     for(i=1;i<=nlstate;i++)
-       fprintf(ficrespop,"# Age");
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+     fprintf(ficresvpl,"%.0f ",age );
+     for(i=1; i<=nlstate;i++)
-       for (cpt=0; cpt<=0;cpt++) {
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+     fprintf(ficresvpl,"\n");
+     free_vector(gp,1,nlstate);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     free_vector(gm,1,nlstate);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+     free_matrix(gradg,1,npar,1,nlstate);
-           nhstepm = nhstepm/hstepm;
+     free_matrix(trgradg,1,nlstate,1,npar);
+   } /* End age */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+   free_vector(xp,1,npar);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ }
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
+ /************ Variance of one-step probabilities  ******************/
-             for(j=1; j<=nlstate+ndeath;j++) {
+ 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[])
-               kk1=0.;kk2=0;
+ {
-               for(i=1; i<=nlstate;i++) {
+   int i, j=0,  k1, l1, tj;
-                 if (mobilav==1)
+   int k2, l2, j1,  z1;
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+   int k=0, l;
-                 else {
+   int first=1, first1, first2;
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-                 }
+   double **dnewm,**doldm;
-               }
+   double *xp;
-               if (h==(int)(calagedatem+12*cpt)){
+   double *gp, *gm;
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+   double **gradg, **trgradg;
-                   /*fprintf(ficrespop," %.3f", kk1);
+   double **mu;
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+   double age, cov[NCOVMAX+1];
-               }
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-             }
+   int theta;
-             for(i=1; i<=nlstate;i++){
+   char fileresprob[FILENAMELENGTH];
-               kk1=0.;
+   char fileresprobcov[FILENAMELENGTH];
-                 for(j=1; j<=nlstate;j++){
+   char fileresprobcor[FILENAMELENGTH];
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+   double ***varpij;
-                 }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+   strcpy(fileresprob,"PROB_");
-             }
+   strcat(fileresprob,fileres);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+     printf("Problem with resultfile: %s\n", fileresprob);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-           }
+   }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   strcpy(fileresprobcov,"PROBCOV_");
-         }
+   strcat(fileresprobcov,fileresu);
-       }
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-   /******/
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+   strcpy(fileresprobcor,"PROBCOR_");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   strcat(fileresprobcor,fileresu);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-           nhstepm = nhstepm/hstepm;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-           oldm=oldms;savm=savms;
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-           for (h=0; h<=nhstepm; h++){
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-             }
+   pstamp(ficresprob);
-             for(j=1; j<=nlstate+ndeath;j++) {
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-               kk1=0.;kk2=0;
+   fprintf(ficresprob,"# Age");
-               for(i=1; i<=nlstate;i++) {
+   pstamp(ficresprobcov);
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-               }
+   fprintf(ficresprobcov,"# Age");
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   pstamp(ficresprobcor);
-             }
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-           }
+   fprintf(ficresprobcor,"# Age");
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
-       }
+   for(i=1; i<=nlstate;i++)
-    }
+     for(j=1; j<=(nlstate+ndeath);j++){
-   }
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
-   if (popforecast==1) {
+  /* fprintf(ficresprob,"\n");
-     free_ivector(popage,0,AGESUP);
+   fprintf(ficresprobcov,"\n");
-     free_vector(popeffectif,0,AGESUP);
+   fprintf(ficresprobcor,"\n");
-     free_vector(popcount,0,AGESUP);
+  */
-   }
+   xp=vector(1,npar);
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   fclose(ficrespop);
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- } /* End of popforecast */
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
- int fileappend(FILE *fichier, char *optionfich)
+   fprintf(ficgp,"\n# Routine varprob");
- {
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   fprintf(fichtm,"\n");
-     printf("Problem with file: %s\n", optionfich);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
-     return (0);
+   fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
-   }
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-   fflush(fichier);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   return (1);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- }
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
- /**************** function prwizard **********************/
+ standard deviations wide on each axis. <br>\
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- {
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   /* Wizard to print covariance matrix template */
+   cov[1]=1;
-   char ca[32], cb[32], cc[32];
+   /* tj=cptcoveff; */
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   tj = (int) pow(2,cptcoveff);
-   int numlinepar;
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   j1=0;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   for(j1=1; j1<=tj;j1++){
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-   for(i=1; i <=nlstate; i++){
+     /*j1++;*/
-     jj=0;
+       if  (cptcovn>0) {
-     for(j=1; j <=nlstate+ndeath; j++){
+         fprintf(ficresprob, "\n#********** Variable ");
-       if(j==i) continue;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       jj++;
+         fprintf(ficresprob, "**********\n#\n");
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+         fprintf(ficresprobcov, "\n#********** Variable ");
-       printf("%1d%1d",i,j);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       fprintf(ficparo,"%1d%1d",i,j);
+         fprintf(ficresprobcov, "**********\n#\n");
-       for(k=1; k<=ncovmodel;k++){
-         /*        printf(" %lf",param[i][j][k]); */
+         fprintf(ficgp, "\n#********** Variable ");
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         printf(" 0.");
+         fprintf(ficgp, "**********\n#\n");
-         fprintf(ficparo," 0.");
-       }
-       printf("\n");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-       fprintf(ficparo,"\n");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     }
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-   }
-   printf("# Scales (for hessian or gradient estimation)\n");
+         fprintf(ficresprobcor, "\n#********** Variable ");
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         fprintf(ficresprobcor, "**********\n#");
-   for(i=1; i <=nlstate; i++){
+       }
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       if(j==i) continue;
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       jj++;
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-       fprintf(ficparo,"%1d%1d",i,j);
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-       printf("%1d%1d",i,j);
+       for (age=bage; age<=fage; age ++){
-       fflush(stdout);
+         cov[2]=age;
-       for(k=1; k<=ncovmodel;k++){
+         if(nagesqr==1)
-         /*      printf(" %le",delti3[i][j][k]); */
+           cov[3]= age*age;
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         for (k=1; k<=cptcovn;k++) {
-         printf(" 0.");
+           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-         fprintf(ficparo," 0.");
+           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-       }
+                                                          * 1  1 1 1 1
-       numlinepar++;
+                                                          * 2  2 1 1 1
-       printf("\n");
+                                                          * 3  1 2 1 1
-       fprintf(ficparo,"\n");
+                                                          */
-     }
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-   }
+         }
-   printf("# Covariance matrix\n");
+         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
- /* # 121 Var(a12)\n\ */
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+         for (k=1; k<=cptcovprod;k++)
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
- /* # 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\ */
+         for(theta=1; theta <=npar; theta++){
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+           for(i=1; i<=npar; i++)
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-   fflush(stdout);
-   fprintf(ficparo,"# Covariance matrix\n");
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   /* # 121 Var(a12)\n\ */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           k=0;
-   /* #   ...\n\ */
+           for(i=1; i<= (nlstate); i++){
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
-   for(itimes=1;itimes<=2;itimes++){
+               gp[k]=pmmij[i][j];
-     jj=0;
+             }
-     for(i=1; i <=nlstate; i++){
+           }
-       for(j=1; j <=nlstate+ndeath; j++){
-         if(j==i) continue;
+           for(i=1; i<=npar; i++)
-         for(k=1; k<=ncovmodel;k++){
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-           jj++;
-           ca[0]= k+'a'-1;ca[1]='\0';
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           if(itimes==1){
+           k=0;
-             printf("#%1d%1d%d",i,j,k);
+           for(i=1; i<=(nlstate); i++){
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+             for(j=1; j<=(nlstate+ndeath);j++){
-           }else{
+               k=k+1;
-             printf("%1d%1d%d",i,j,k);
+               gm[k]=pmmij[i][j];
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             }
-             /*  printf(" %.5le",matcov[i][j]); */
+           }
-           }
-           ll=0;
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-           for(li=1;li <=nlstate; li++){
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+         }
-               if(lj==li) continue;
-               for(lk=1;lk<=ncovmodel;lk++){
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                 ll++;
+           for(theta=1; theta <=npar; theta++)
-                 if(ll<=jj){
+             trgradg[j][theta]=gradg[theta][j];
-                   cb[0]= lk +'a'-1;cb[1]='\0';
-                   if(ll<jj){
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                     if(itimes==1){
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     }else{
-                       printf(" 0.");
+         k=0;
-                       fprintf(ficparo," 0.");
+         for(i=1; i<=(nlstate); i++){
-                     }
+           for(j=1; j<=(nlstate+ndeath);j++){
-                   }else{
+             k=k+1;
-                     if(itimes==1){
+             mu[k][(int) age]=pmmij[i][j];
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+           }
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+         }
-                     }else{
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                       printf(" 0.");
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                       fprintf(ficparo," 0.");
+             varpij[i][j][(int)age] = doldm[i][j];
-                     }
-                   }
+         /*printf("\n%d ",(int)age);
-                 }
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-               } /* end lk */
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-             } /* end lj */
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           } /* end li */
+           }*/
-           printf("\n");
-           fprintf(ficparo,"\n");
+         fprintf(ficresprob,"\n%d ",(int)age);
-           numlinepar++;
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-         } /* end k*/
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-       } /*end j */
-     } /* end i */
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-   } /* end itimes */
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- } /* end of prwizard */
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
- /******************* Gompertz Likelihood ******************************/
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
- double gompertz(double x[])
+         }
- {
+         i=0;
-   double A,B,L=0.0,sump=0.,num=0.;
+         for (k=1; k<=(nlstate);k++){
-   int i,n=0; /* n is the size of the sample */
+           for (l=1; l<=(nlstate+ndeath);l++){
+             i++;
-   for (i=0;i<=imx-1 ; i++) {
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-     sump=sump+weight[i];
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-     /*    sump=sump+1;*/
+             for (j=1; j<=i;j++){
-     num=num+1;
+               /* 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]);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
-   /* 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]);*/
+         }/* end of loop for state */
+       } /* end of loop for age */
-   for (i=1;i<=imx ; i++)
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-     {
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-       if (cens[i] == 1 && wav[i]>1)
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       if (cens[i] == 0 && wav[i]>1)
+       /* Confidence intervalle of pij  */
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+       /*
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+         fprintf(ficgp,"\nunset parametric;unset label");
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-       if (wav[i] > 1 ) { /* ??? */
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-         L=L+A*weight[i];
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-       }
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-     }
+       */
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;first2=2;
-   return -2*L*num/sump;
+       for (k2=1; k2<=(nlstate);k2++){
- }
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
- /******************* Printing html file ***********/
+           j=(k2-1)*(nlstate+ndeath)+l2;
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+           for (k1=1; k1<=(nlstate);k1++){
-                   int lastpass, int stepm, int weightopt, char model[],\
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-                   int imx,  double p[],double **matcov,double agemortsup){
+               if(l1==k1) continue;
-   int i,k;
+               i=(k1-1)*(nlstate+ndeath)+l1;
+               if(i<=j) continue;
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+               for (age=bage; age<=fage; age ++){
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+                 if ((int)age %5==0){
-   for (i=1;i<=2;i++)
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-     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]));
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-   fprintf(fichtm,"</ul>");
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
-  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>");
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-  for (k=agegomp;k<(agemortsup-2);k++)
+                   if ((lc2 <0) || (lc1 <0) ){
-    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]);
+                     if(first2==1){
+                       first1=0;
+                     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);
-   fflush(fichtm);
+                     }
- }
+                     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);
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
- /******************* Gnuplot file **************/
+                     /* lc2=fabs(lc2); */
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+                   }
-   char dirfileres[132],optfileres[132];
+                   /* Eigen vectors */
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-   int ng;
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
+                   v12=-v21;
-   /*#ifdef windows */
+                   v22=v11;
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+                   tnalp=v21/v11;
-     /*#endif */
+                   if(first1==1){
+                     first1=0;
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-   strcpy(dirfileres,optionfilefiname);
+                   }
-   strcpy(optfileres,"vpl");
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+                   /*printf(fignu*/
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-   fprintf(ficgp, "set ter png small\n set log y\n");
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-   fprintf(ficgp, "set size 0.65,0.65\n");
+                   if(first==1){
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+                     first=0;
+                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
- }
+                     fprintf(ficgp,"\nset parametric;unset label");
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter svg size 640, 480");
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
- /***********************************************/
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
- /**************** Main Program *****************/
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- /***********************************************/
+                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
- int main(int argc, char *argv[])
+                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- {
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+                     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",\
-   int linei, month, year,iout;
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   int jj, ll, li, lj, lk, imk;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   int numlinepar=0; /* Current linenumber of parameter file */
+                   }else{
-   int itimes;
+                     first=0;
-   int NDIM=2;
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   char ca[32], cb[32], cc[32];
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   char dummy[]="                         ";
+                     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",\
-   /*  FILE *fichtm; *//* Html File */
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   /* FILE *ficgp;*/ /*Gnuplot File */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   struct stat info;
+                   }/* if first */
-   double agedeb, agefin,hf;
+                 } /* age mod 5 */
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+               } /* end loop age */
+               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-   double fret;
+               first=1;
-   double **xi,tmp,delta;
+             } /*l12 */
+           } /* k12 */
-   double dum; /* Dummy variable */
+         } /*l1 */
-   double ***p3mat;
+       }/* k1 */
-   double ***mobaverage;
+       /* } */ /* loop covariates */
-   int *indx;
+   }
-   char line[MAXLINE], linepar[MAXLINE];
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   char pathr[MAXLINE], pathimach[MAXLINE];
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   char **bp, *tok, *val; /* pathtot */
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   int firstobs=1, lastobs=10;
+   free_vector(xp,1,npar);
-   int sdeb, sfin; /* Status at beginning and end */
+   fclose(ficresprob);
-   int c,  h , cpt,l;
+   fclose(ficresprobcov);
-   int ju,jl, mi;
+   fclose(ficresprobcor);
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   fflush(ficgp);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   fflush(fichtmcov);
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+ }
-   int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
-   int agemortsup;
+ /******************* Printing html file ***********/
-   float  sumlpop=0.;
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+                   int lastpass, int stepm, int weightopt, char model[],\
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   int popforecast, int estepm ,\
-   double bage, fage, age, agelim, agebase;
+                   double jprev1, double mprev1,double anprev1, \
-   double ftolpl=FTOL;
+                   double jprev2, double mprev2,double anprev2){
-   double **prlim;
+   int jj1, k1, i1, cpt;
-   double *severity;
-   double ***param; /* Matrix of parameters */
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   double  *p;
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   double **matcov; /* Matrix of covariance */
+ </ul>");
-   double ***delti3; /* Scale */
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-   double *delti; /* Scale */
+  - 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 ***eij, ***vareij;
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
-   double **varpl; /* Variances of prevalence limits by age */
+    fprintf(fichtm,"\
-   double *epj, vepp;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-   double kk1, kk2;
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+    fprintf(fichtm,"\
-   double **ximort;
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
-   int *dcwave;
+    fprintf(fichtm,"\
+  - (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): \
-   char z[1]="c", occ;
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+    fprintf(fichtm,"\
-   char  *strt, strtend[80];
+  - Population projections by age and states: \
-   char *stratrunc;
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
-   int lstra;
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   long total_usecs;
+  m=pow(2,cptcoveff);
- /*   setlocale (LC_ALL, ""); */
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
- /*   textdomain (PACKAGE); */
+  jj1=0;
- /*   setlocale (LC_CTYPE, ""); */
+  for(k1=1; k1<=m;k1++){
- /*   setlocale (LC_MESSAGES, ""); */
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+      jj1++;
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+      if (cptcovn > 0) {
-   (void) gettimeofday(&start_time,&tzp);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   curr_time=start_time;
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-   tm = *localtime(&start_time.tv_sec);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
-   tmg = *gmtime(&start_time.tv_sec);
+          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
-   strcpy(strstart,asctime(&tm));
+        }
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
- /*  printf("Localtime (at start)=%s",strstart); */
+      }
- /*  tp.tv_sec = tp.tv_sec +86400; */
+      /* aij, bij */
- /*  tm = *localtime(&start_time.tv_sec); */
+      fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+      /* Pij */
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+      fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
- /*   tp.tv_sec = mktime(&tmg); */
+ <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
- /*   strt=asctime(&tmg); */
+      /* Quasi-incidences */
- /*   printf("Time(after) =%s",strstart);  */
+      fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- /*  (void) time (&time_value);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
- *  tm = *localtime(&time_value);
+ divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
- *  strstart=asctime(&tm);
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+      /* Survival functions (period) in state j */
- */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
-   nberr=0; /* Number of errors and warnings */
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
-   nbwarn=0;
+      }
-   getcwd(pathcd, size);
+      /* State specific survival functions (period) */
+      for(cpt=1; cpt<=nlstate;cpt++){
-   printf("\n%s\n%s",version,fullversion);
+        fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
-   if(argc <=1){
+  Or probability to survive in various states (1 to %d) being in state %d at different ages.\
-     printf("\nEnter the parameter file name: ");
+  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
-     fgets(pathr,FILENAMELENGTH,stdin);
+      }
-     i=strlen(pathr);
+      /* Period (stable) prevalence in each health state */
-     if(pathr[i-1]=='\n')
+      for(cpt=1; cpt<=nlstate;cpt++){
-       pathr[i-1]='\0';
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
-    for (tok = pathr; tok != NULL; ){
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
-       printf("Pathr |%s|\n",pathr);
+      }
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+      for(cpt=1; cpt<=nlstate;cpt++) {
-       printf("val= |%s| pathr=%s\n",val,pathr);
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
-       strcpy (pathtot, val);
+ <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
-       if(pathr[0] == '\0') break; /* Dirty */
+      }
-     }
+    /* } /\* end i1 *\/ */
-   }
+  }/* End k1 */
-   else{
+  fprintf(fichtm,"</ul>");
-     strcpy(pathtot,argv[1]);
-   }
+  fprintf(fichtm,"\
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-   /*cygwin_split_path(pathtot,path,optionfile);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
-   /* cutv(path,optionfile,pathtot,'\\');*/
+ But because parameters are usually highly correlated (a higher incidence of disability \
+ and a higher incidence of recovery can give very close observed transition) it might \
-   /* Split argv[0], imach program to get pathimach */
+ be very useful to look not only at linear confidence intervals estimated from the \
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ covariance matrix of the one-step probabilities. \
-  /*   strcpy(pathimach,argv[0]); */
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-   chdir(path); /* Can be a relative path */
+  fprintf(fichtm,"\
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     printf("Current directory %s!\n",pathcd);
+          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-   strcpy(command,"mkdir ");
-   strcat(command,optionfilefiname);
+  fprintf(fichtm,"\
-   if((outcmd=system(command)) != 0){
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+  fprintf(fichtm,"\
-     /* fclose(ficlog); */
+  - 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): \
- /*     exit(1); */
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   }
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+  fprintf(fichtm,"\
- /*     perror("mkdir"); */
+  - (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>",
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-   /*-------- arguments in the command line --------*/
+  fprintf(fichtm,"\
+  - 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 file */
+          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-   strcat(filelog, optionfilefiname);
+  fprintf(fichtm,"\
-   strcat(filelog,".log");    /* */
+  - 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((ficlog=fopen(filelog,"w"))==NULL)    {
+          estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-     printf("Problem with logfile %s\n",filelog);
+  fprintf(fichtm,"\
-     goto end;
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-   }
+          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
-   fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-  path=%s \n\
+ /*      <br>",fileres,fileres,fileres,fileres); */
-  optionfile=%s\n\
+ /*  else  */
-  optionfilext=%s\n\
+ /*    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); */
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   printf("Local time (at start):%s",strstart);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+  m=pow(2,cptcoveff);
-   fflush(ficlog);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
-   /* */
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-   strcpy(fileres,"r");
+      jj1++;
-   strcat(fileres, optionfilefiname);
+      if (cptcovn > 0) {
-   strcat(fileres,".txt");    /* Other files have txt extension */
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   /*---------arguments file --------*/
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+      }
-     printf("Problem with optionfile %s\n",optionfile);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-     fflush(ficlog);
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
-     goto end;
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
-   }
+      }
+      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\
-   strcpy(filereso,"o");
+  drawn in addition to the population based expectancies computed using\
-   strcat(filereso,fileres);
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg<br>\
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-     printf("Problem with Output resultfile: %s\n", filereso);
+    /* } /\* end i1 *\/ */
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+  }/* End k1 */
-     fflush(ficlog);
+  fprintf(fichtm,"</ul>");
-     goto end;
+  fflush(fichtm);
-   }
+ }
-   /* Reads comments: lines beginning with '#' */
+ /******************* Gnuplot file **************/
-   numlinepar=0;
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   char dirfileres[132],optfileres[132];
-     fgets(line, MAXLINE, ficpar);
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-     numlinepar++;
+   int ng=0;
-     puts(line);
+   int vpopbased;
-     fputs(line,ficparo);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     fputs(line,ficlog);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   }
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-   ungetc(c,ficpar);
+ /*   } */
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   /*#ifdef windows */
-   numlinepar++;
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   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);
+     /*#endif */
-   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);
+   m=pow(2,cptcoveff);
-   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);
-   fflush(ficlog);
+   /* Contribution to likelihood */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   /* Plot the probability implied in the likelihood */
-     ungetc(c,ficpar);
+     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
-     fgets(line, MAXLINE, ficpar);
+     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
-     numlinepar++;
+     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
-     puts(line);
+     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
-     fputs(line,ficparo);
+ /* nice for mle=4 plot by number of matrix products.
-     fputs(line,ficlog);
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
-   }
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
-   ungetc(c,ficpar);
+     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
-   covar=matrix(0,NCOVMAX,1,n);
+     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+     for (i=1; i<= nlstate ; i ++) {
+       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       fprintf(ficgp,"  u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       for (j=2; j<= nlstate+ndeath ; j ++) {
+         fprintf(ficgp,",\\\n \"\" u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       }
-   delti=delti3[1][1];
+       fprintf(ficgp,";\nset out; unset ylabel;\n");
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+     }
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficgp,"\nset out;unset log\n");
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
-     fclose (ficparo);
-     fclose (ficlog);
+   strcpy(dirfileres,optionfilefiname);
-     goto end;
+   strcpy(optfileres,"vpl");
-     exit(0);
+  /* 1eme*/
-   }
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
-   else if(mle==-3) {
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+      fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-     matcov=matrix(1,npar,1,npar);
+ set ylabel \"Probability\" \n\
-   }
+ set ter svg size 640, 480\n\
-   else{
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-     /* Read guess parameters */
-     /* Reads comments: lines beginning with '#' */
+      for (i=1; i<= nlstate ; i ++) {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       ungetc(c,ficpar);
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-       fgets(line, MAXLINE, ficpar);
+      }
-       numlinepar++;
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-       puts(line);
+      for (i=1; i<= nlstate ; i ++) {
-       fputs(line,ficparo);
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       fputs(line,ficlog);
+        else fprintf(ficgp," %%*lf (%%*lf)");
-     }
+      }
-     ungetc(c,ficpar);
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     for(i=1; i <=nlstate; i++){
+        else fprintf(ficgp," %%*lf (%%*lf)");
-       j=0;
+      }
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-         if(jj==i) continue;
+      fprintf(ficgp,"\nset out \n");
-         j++;
+     } /* k1 */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   } /* cpt */
-         if ((i1 != i) && (j1 != j)){
+   /*2 eme*/
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
- It might be a problem of design; if ncovcol and the model are correct\n \
+   for (k1=1; k1<= m ; k1 ++) {
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-           exit(1);
+     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-         }
+       if(vpopbased==0)
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-         if(mle==1)
+       else
-           printf("%1d%1d",i,j);
+         fprintf(ficgp,"\nreplot ");
-         fprintf(ficlog,"%1d%1d",i,j);
+       for (i=1; i<= nlstate+1 ; i ++) {
-         for(k=1; k<=ncovmodel;k++){
+         k=2*i;
-           fscanf(ficpar," %lf",&param[i][j][k]);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-           if(mle==1){
+         for (j=1; j<= nlstate+1 ; j ++) {
-             printf(" %lf",param[i][j][k]);
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-             fprintf(ficlog," %lf",param[i][j][k]);
+           else fprintf(ficgp," %%*lf (%%*lf)");
-           }
+         }
-           else
+         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-             fprintf(ficlog," %lf",param[i][j][k]);
+         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-           fprintf(ficparo," %lf",param[i][j][k]);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         }
+         for (j=1; j<= nlstate+1 ; j ++) {
-         fscanf(ficpar,"\n");
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-         numlinepar++;
+           else fprintf(ficgp," %%*lf (%%*lf)");
-         if(mle==1)
+         }
-           printf("\n");
+         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficlog,"\n");
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         fprintf(ficparo,"\n");
+         for (j=1; j<= nlstate+1 ; j ++) {
-       }
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-     }
+           else fprintf(ficgp," %%*lf (%%*lf)");
-     fflush(ficlog);
+         }
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-     p=param[1][1];
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+       } /* state */
-     /* Reads comments: lines beginning with '#' */
+     } /* vpopbased */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-       ungetc(c,ficpar);
+   } /* k1 */
-       fgets(line, MAXLINE, ficpar);
+   /*3eme*/
-       numlinepar++;
-       puts(line);
+   for (k1=1; k1<= m ; k1 ++) {
-       fputs(line,ficparo);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fputs(line,ficlog);
+       /*       k=2+nlstate*(2*cpt-2); */
-     }
+       k=2+(nlstate+1)*(cpt-1);
-     ungetc(c,ficpar);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+       fprintf(ficgp,"set ter svg size 640, 480\n\
-     for(i=1; i <=nlstate; i++){
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         if ((i1-i)*(j1-j)!=0){
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-           exit(1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-         printf("%1d%1d",i,j);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       */
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       for (i=1; i< nlstate ; i ++) {
-         for(k=1; k<=ncovmodel;k++){
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+       }
-           fprintf(ficlog," %le",delti3[i][j][k]);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
-         }
+     }
-         fscanf(ficpar,"\n");
+   }
-         numlinepar++;
-         printf("\n");
+   /* Survival functions (period) from state i in state j by initial state i */
-         fprintf(ficparo,"\n");
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-         fprintf(ficlog,"\n");
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-       }
+       k=3;
-     }
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
-     fflush(ficlog);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-     delti=delti3[1][1];
+ set ter svg size 640, 480\n\
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+       for (i=1; i<= nlstate ; i ++){
+         if(i==1)
-     /* Reads comments: lines beginning with '#' */
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         else
-       ungetc(c,ficpar);
+           fprintf(ficgp,", '' ");
-       fgets(line, MAXLINE, ficpar);
+         l=(nlstate+ndeath)*(i-1)+1;
-       numlinepar++;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-       puts(line);
+         for (j=2; j<= nlstate+ndeath ; j ++)
-       fputs(line,ficparo);
+           fprintf(ficgp,"+$%d",k+l+j-1);
-       fputs(line,ficlog);
+         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
-     }
+       } /* nlstate */
-     ungetc(c,ficpar);
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
-     matcov=matrix(1,npar,1,npar);
+   } /* end covariate */
-     for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",&str);
+   /* Survival functions (period) from state i in state j by final state j */
-       if(mle==1)
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
-         printf("%s",str);
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
-       fprintf(ficlog,"%s",str);
+       k=3;
-       fprintf(ficparo,"%s",str);
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-       for(j=1; j <=i; j++){
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
-         fscanf(ficpar," %le",&matcov[i][j]);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-         if(mle==1){
+ set ter svg size 640, 480\n\
-           printf(" %.5le",matcov[i][j]);
+ unset log y\n\
-         }
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-         fprintf(ficlog," %.5le",matcov[i][j]);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-         fprintf(ficparo," %.5le",matcov[i][j]);
+         if(j==1)
-       }
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-       fscanf(ficpar,"\n");
+         else
-       numlinepar++;
+           fprintf(ficgp,", '' ");
-       if(mle==1)
+         l=(nlstate+ndeath)*(cpt-1) +j;
-         printf("\n");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-       fprintf(ficlog,"\n");
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
-       fprintf(ficparo,"\n");
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-     }
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-     for(i=1; i <=npar; i++)
+       } /* nlstate */
-       for(j=i+1;j<=npar;j++)
+       fprintf(ficgp,", '' ");
-         matcov[i][j]=matcov[j][i];
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-     if(mle==1)
+         l=(nlstate+ndeath)*(cpt-1) +j;
-       printf("\n");
+         if(j < nlstate)
-     fprintf(ficlog,"\n");
+           fprintf(ficgp,"$%d +",k+l);
+         else
-     fflush(ficlog);
+           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+       }
-     /*-------- Rewriting parameter file ----------*/
+       fprintf(ficgp,"\nset out\n");
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+     } /* end cpt state*/
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+   } /* end covariate */
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   /* CV preval stable (period) for each covariate */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       k=3;
-     }
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
-     fprintf(ficres,"#%s\n",version);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
-   }    /* End of mle != -3 */
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n\
-   /*-------- data file ----------*/
+ unset log y\n\
-   if((fic=fopen(datafile,"r"))==NULL)    {
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+       for (i=1; i<= nlstate ; i ++){
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+         if(i==1)
-   }
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
-   n= lastobs;
+           fprintf(ficgp,", '' ");
-   severity = vector(1,maxwav);
+         l=(nlstate+ndeath)*(i-1)+1;
-   outcome=imatrix(1,maxwav+1,1,n);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   num=lvector(1,n);
+         for (j=2; j<= nlstate ; j ++)
-   moisnais=vector(1,n);
+           fprintf(ficgp,"+$%d",k+l+j-1);
-   annais=vector(1,n);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-   moisdc=vector(1,n);
+       } /* nlstate */
-   andc=vector(1,n);
+       fprintf(ficgp,"\nset out\n");
-   agedc=vector(1,n);
+     } /* end cpt state*/
-   cod=ivector(1,n);
+   } /* end covariate */
-   weight=vector(1,n);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   /* proba elementaires */
-   mint=matrix(1,maxwav,1,n);
+   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
-   anint=matrix(1,maxwav,1,n);
+   for(i=1,jk=1; i <=nlstate; i++){
-   s=imatrix(1,maxwav+1,1,n);
+     fprintf(ficgp,"# initial state %d\n",i);
-   tab=ivector(1,NCOVMAX);
+     for(k=1; k <=(nlstate+ndeath); k++){
-   ncodemax=ivector(1,8);
+       if (k != i) {
+         fprintf(ficgp,"#   current state %d\n",k);
-   i=1;
+         for(j=1; j <=ncovmodel; j++){
-   linei=0;
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+           jk++;
-     linei=linei+1;
+         }
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+         fprintf(ficgp,"\n");
-       if(line[j] == '\t')
+       }
-         line[j] = ' ';
+     }
-     }
+    }
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   fprintf(ficgp,"##############\n#\n");
-       ;
-     };
+   /*goto avoid;*/
-     line[j+1]=0;  /* Trims blanks at end of line */
+   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
-     if(line[0]=='#'){
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
-       fprintf(ficlog,"Comment line\n%s\n",line);
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-       printf("Comment line\n%s\n",line);
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-       continue;
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-     }
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-     for (j=maxwav;j>=1;j--){
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-       cutv(stra, strb,line,' ');
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-       errno=0;
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
-       lval=strtol(strb,&endptr,10);
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+   fprintf(ficgp,"#\n");
-         exit(1);
+    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-       }
+      fprintf(ficgp,"# ng=%d\n",ng);
-       s[j][i]=lval;
+      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+      for(jk=1; jk <=m; jk++) {
-       strcpy(line,stra);
+        fprintf(ficgp,"#    jk=%d\n",jk);
-       cutv(stra, strb,line,' ');
+        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+        fprintf(ficgp,"\nset ter svg size 640, 480 ");
-       }
+        if (ng==1){
-       else  if(iout=sscanf(strb,"%s.") != 0){
+          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
-         month=99;
+          fprintf(ficgp,"\nunset log y");
-         year=9999;
+        }else if (ng==2){
-       }else{
+          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+          fprintf(ficgp,"\nset log y");
-         exit(1);
+        }else if (ng==3){
-       }
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-       anint[j][i]= (double) year;
+          fprintf(ficgp,"\nset log y");
-       mint[j][i]= (double)month;
+        }else
-       strcpy(line,stra);
+          fprintf(ficgp,"\nunset title ");
-     } /* ENd Waves */
+        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        i=1;
-     cutv(stra, strb,line,' ');
+        for(k2=1; k2<=nlstate; k2++) {
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+          k3=i;
-     }
+          for(k=1; k<=(nlstate+ndeath); k++) {
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+            if (k != k2){
-       month=99;
+              switch( ng) {
-       year=9999;
+              case 1:
-     }else{
+                if(nagesqr==0)
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+                  fprintf(ficgp," p%d+p%d*x",i,i+1);
-       exit(1);
+                else /* nagesqr =1 */
-     }
+                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-     andc[i]=(double) year;
+                break;
-     moisdc[i]=(double) month;
+              case 2: /* ng=2 */
-     strcpy(line,stra);
+                if(nagesqr==0)
+                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-     cutv(stra, strb,line,' ');
+                else /* nagesqr =1 */
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-     }
+                break;
-     else  if(iout=sscanf(strb,"%s.") != 0){
+              case 3:
-       month=99;
+                if(nagesqr==0)
-       year=9999;
+                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-     }else{
+                else /* nagesqr =1 */
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
-       exit(1);
+                break;
-     }
+              }
-     annais[i]=(double)(year);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-     moisnais[i]=(double)(month);
+              for(j=3; j <=ncovmodel-nagesqr; j++) {
-     strcpy(line,stra);
+                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+                if(ij <=cptcovage) { /* Bug valgrind */
-     cutv(stra, strb,line,' ');
+                  if((j-2)==Tage[ij]) { /* Bug valgrind */
-     errno=0;
+                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-     dval=strtod(strb,&endptr);
+                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-     if( strb[0]=='\0' || (*endptr != '\0')){
+                    ij++;
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+                  }
-       exit(1);
+                }
-     }
+                else
-     weight[i]=dval;
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-     strcpy(line,stra);
+              }
+              if(ng != 1){
-     for (j=ncovcol;j>=1;j--){
+                fprintf(ficgp,")/(1");
-       cutv(stra, strb,line,' ');
-       errno=0;
+                for(k1=1; k1 <=nlstate; k1++){
-       lval=strtol(strb,&endptr,10);
+                  if(nagesqr==0)
-       if( strb[0]=='\0' || (*endptr != '\0')){
+                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-         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);
+                  else /* nagesqr =1 */
-         exit(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(lval <-1 || lval >1){
+                  ij=1;
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+                  for(j=3; j <=ncovmodel-nagesqr; j++){
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+                    if(ij <=cptcovage) { /* Bug valgrind */
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+                      if((j-2)==Tage[ij]) { /* Bug valgrind */
-  For example, for multinomial values like 1, 2 and 3,\n \
+                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-  build V1=0 V2=0 for the reference value (1),\n \
+                        /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-         V1=1 V2=0 for (2) \n \
+                        ij++;
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+                      }
-  output of IMaCh is often meaningless.\n \
+                    }
-  Exiting.\n",lval,linei, i,line,j);
+                    else
-         exit(1);
+                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
-       }
+                  }
-       covar[j][i]=(double)(lval);
+                  fprintf(ficgp,")");
-       strcpy(line,stra);
+                }
-     }
+                fprintf(ficgp,")");
-     lstra=strlen(stra);
+                if(ng ==2)
+                  fprintf(ficgp," t \"p%d%d\" ", k2,k);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+                else /* ng= 3 */
-       stratrunc = &(stra[lstra-9]);
+                  fprintf(ficgp," t \"i%d%d\" ", k2,k);
-       num[i]=atol(stratrunc);
+              }else{ /* end ng <> 1 */
-     }
+                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
-     else
+              }
-       num[i]=atol(stra);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+              i=i+ncovmodel;
-       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;}*/
+            }
+          } /* end k */
-     i=i+1;
+        } /* end k2 */
-   } /* End loop reading  data */
+        fprintf(ficgp,"\n set out\n");
-   fclose(fic);
+      } /* end jk */
-   /* printf("ii=%d", ij);
+    } /* end ng */
-      scanf("%d",i);*/
+  /* avoid: */
-   imx=i-1; /* Number of individuals */
+    fflush(ficgp);
+ }  /* end gnuplot */
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+ /*************** Moving average **************/
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-     }*/
-    /*  for (i=1; i<=imx; i++){
+   int i, cpt, cptcod;
-      if (s[4][i]==9)  s[4][i]=-1;
+   int modcovmax =1;
-      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]));}*/
+   int mobilavrange, mob;
+   double age;
-   /* for (i=1; i<=imx; i++) */
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+                            a covariate has 2 modalities */
-      else weight[i]=1;*/
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-   /* Calculation of the number of parameters from char model */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+     if(mobilav==1) mobilavrange=5; /* default */
-   Tprod=ivector(1,15);
+     else mobilavrange=mobilav;
-   Tvaraff=ivector(1,15);
+     for (age=bage; age<=fage; age++)
-   Tvard=imatrix(1,15,1,2);
+       for (i=1; i<=nlstate;i++)
-   Tage=ivector(1,15);
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     /* We keep the original values on the extreme ages bage, fage and for
-     j=0, j1=0, k1=1, k2=1;
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-     j=nbocc(model,'+'); /* j=Number of '+' */
+        we use a 5 terms etc. until the borders are no more concerned.
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     */
-     cptcovn=j+1;
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-     cptcovprod=j1; /*Number of products */
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+         for (i=1; i<=nlstate;i++){
-     strcpy(modelsav,model);
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-       printf("Error. Non available option model=%s ",model);
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-       goto end;
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-     }
+               }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-     /* This loop fills the array Tvar from the string 'model'.*/
+           }
+         }
-     for(i=(j+1); i>=1;i--){
+       }/* end age */
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+     }/* end mob */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   }else return -1;
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+   return 0;
-       /*scanf("%d",i);*/
+ }/* End movingaverage */
-       if (strchr(strb,'*')) {  /* Model includes a product */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+ /************** Forecasting ******************/
-           cptcovprod--;
+ 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){
-           cutv(strb,stre,strd,'V');
+   /* proj1, year, month, day of starting projection
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+      agemin, agemax range of age
-           cptcovage++;
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-             Tage[cptcovage]=i;
+      anproj2 year of en of projection (same day and month as proj1).
-             /*printf("stre=%s ", stre);*/
+   */
-         }
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+   double agec; /* generic age */
-           cptcovprod--;
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-           cutv(strb,stre,strc,'V');
+   double *popeffectif,*popcount;
-           Tvar[i]=atoi(stre);
+   double ***p3mat;
-           cptcovage++;
+   double ***mobaverage;
-           Tage[cptcovage]=i;
+   char fileresf[FILENAMELENGTH];
-         }
-         else {  /* Age is not in the model */
+   agelim=AGESUP;
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+   strcpy(fileresf,"F_");
-           Tprod[k1]=i;
+   strcat(fileresf,fileresu);
-           Tvard[k1][1]=atoi(strc); /* m*/
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-           Tvard[k1][2]=atoi(stre); /* n */
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+   }
-           for (k=1; k<=lastobs;k++)
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-           k1++;
-           k2=k2+2;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-         }
-       }
+   if (mobilav!=0) {
-       else { /* no more sum */
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-        /*  scanf("%d",i);*/
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       cutv(strd,strc,strb,'V');
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       Tvar[i]=atoi(strc);
+     }
-       }
+   }
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-         scanf("%d",i);*/
+   if (stepm<=12) stepsize=1;
-     } /* end of loop + */
+   if(estepm < stepm){
-   } /* end model */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+   else  hstepm=estepm;
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   hstepm=hstepm/stepm;
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-   printf("cptcovprod=%d ", cptcovprod);
+                                fractional in yp1 */
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
-   scanf("%d ",i);*/
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-     /*  if(mle==1){*/
+   jprojmean=yp;
-   if (weightopt != 1) { /* Maximisation without weights*/
+   if(jprojmean==0) jprojmean=1;
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   if(mprojmean==0) jprojmean=1;
-   }
-     /*-calculation of age at interview from date of interview and age at death -*/
+   i1=cptcoveff;
-   agev=matrix(1,maxwav,1,imx);
+   if (cptcovn < 1){i1=1;}
-   for (i=1; i<=imx; i++) {
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-     for(m=2; (m<= maxwav); m++) {
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-         anint[m][i]=9999;
-         s[m][i]=-1;
+ /*            if (h==(int)(YEARM*yearp)){ */
-       }
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-         nberr++;
+       k=k+1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+       fprintf(ficresf,"\n#******");
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+       for(j=1;j<=cptcoveff;j++) {
-         s[m][i]=-1;
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+       fprintf(ficresf,"******\n");
-         nberr++;
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+       for(j=1; j<=nlstate+ndeath;j++){
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         for(i=1; i<=nlstate;i++)
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+           fprintf(ficresf," p%d%d",i,j);
-       }
+         fprintf(ficresf," p.%d",j);
-     }
+       }
-   }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+         fprintf(ficresf,"\n");
-   for (i=1; i<=imx; i++)  {
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     for(m=firstpass; (m<= lastpass); m++){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-         if (s[m][i] >= nlstate+1) {
+           nhstepm = nhstepm/hstepm;
-           if(agedc[i]>0)
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+           oldm=oldms;savm=savms;
-               agev[m][i]=agedc[i];
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
+           for (h=0; h<=nhstepm; h++){
-               if ((int)andc[i]!=9999){
+             if (h*hstepm/YEARM*stepm ==yearp) {
-                 nbwarn++;
+               fprintf(ficresf,"\n");
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+               for(j=1;j<=cptcoveff;j++)
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                 agev[m][i]=-1;
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-               }
+             }
-             }
+             for(j=1; j<=nlstate+ndeath;j++) {
-         }
+               ppij=0.;
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+               for(i=1; i<=nlstate;i++) {
-                                  years but with the precision of a month */
+                 if (mobilav==1)
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+                 else {
-             agev[m][i]=1;
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-           else if(agev[m][i] <agemin){
+                 }
-             agemin=agev[m][i];
+                 if (h*hstepm/YEARM*stepm== yearp) {
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-           }
+                 }
-           else if(agev[m][i] >agemax){
+               } /* end i */
-             agemax=agev[m][i];
+               if (h*hstepm/YEARM*stepm==yearp) {
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+                 fprintf(ficresf," %.3f", ppij);
-           }
+               }
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+             }/* end j */
-           /*     agev[m][i] = age[i]+2*m;*/
+           } /* end h */
-         }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         else { /* =9 */
+         } /* end agec */
-           agev[m][i]=1;
+       } /* end yearp */
-           s[m][i]=-1;
+     } /* end cptcod */
-         }
+   } /* end  cptcov */
-       }
-       else /*= 0 Unknown */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         agev[m][i]=1;
-     }
+   fclose(ficresf);
+ }
-   }
-   for (i=1; i<=imx; i++)  {
+ /************** Forecasting *****not tested NB*************/
-     for(m=firstpass; (m<=lastpass); m++){
+ 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){
-       if (s[m][i] > (nlstate+ndeath)) {
-         nberr++;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-         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);
+   int *popage;
-         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);
+   double calagedatem, agelim, kk1, kk2;
-         goto end;
+   double *popeffectif,*popcount;
-       }
+   double ***p3mat,***tabpop,***tabpopprev;
-     }
+   double ***mobaverage;
-   }
+   char filerespop[FILENAMELENGTH];
-   /*for (i=1; i<=imx; i++){
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   for (m=firstpass; (m<lastpass); m++){
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+   agelim=AGESUP;
- }
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
- }*/
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   strcpy(filerespop,"POP_");
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   strcat(filerespop,fileresu);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   agegomp=(int)agemin;
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   free_vector(severity,1,maxwav);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   free_imatrix(outcome,1,maxwav+1,1,n);
+   }
-   free_vector(moisnais,1,n);
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   free_vector(annais,1,n);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   /* free_matrix(mint,1,maxwav,1,n);
-      free_matrix(anint,1,maxwav,1,n);*/
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   free_vector(moisdc,1,n);
-   free_vector(andc,1,n);
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   wav=ivector(1,imx);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+     }
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   }
-   /* Concatenates waves */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   if (stepm<=12) stepsize=1;
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   agelim=AGESUP;
-   Tcode=ivector(1,100);
+   hstepm=1;
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   hstepm=hstepm/stepm;
-   ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+       printf("Problem with population file : %s\n",popfile);exit(0);
-                                  the estimations*/
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   h=0;
+     }
-   m=pow(2,cptcoveff);
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
-   for(k=1;k<=cptcoveff; k++){
+     popcount=vector(0,AGESUP);
-     for(i=1; i <=(m/pow(2,k));i++){
-       for(j=1; j <= ncodemax[k]; j++){
+     i=1;
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-           h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+     imx=i;
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-         }
+   }
-       }
-     }
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-   }
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+       k=k+1;
-      codtab[1][2]=1;codtab[2][2]=2; */
+       fprintf(ficrespop,"\n#******");
-   /* for(i=1; i <=m ;i++){
+       for(j=1;j<=cptcoveff;j++) {
-      for(k=1; k <=cptcovn; k++){
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+       }
-      }
+       fprintf(ficrespop,"******\n");
-      printf("\n");
+       fprintf(ficrespop,"# Age");
-      }
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-      scanf("%d",i);*/
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-   /*------------ gnuplot -------------*/
+       for (cpt=0; cpt<=0;cpt++) {
-   strcpy(optionfilegnuplot,optionfilefiname);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   strcat(optionfilegnuplot,".gp");
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-     printf("Problem with file %s",optionfilegnuplot);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
+           oldm=oldms;savm=savms;
-   else{
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+           for (h=0; h<=nhstepm; h++){
-     fprintf(ficgp,"set missing 'NaNq'\n");
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   }
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   /*  fclose(ficgp);*/
+             }
-   /*--------- index.htm --------*/
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+               for(i=1; i<=nlstate;i++) {
-   if(mle==-3)
+                 if (mobilav==1)
-     strcat(optionfilehtm,"-mort");
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   strcat(optionfilehtm,".htm");
+                 else {
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+                 }
-   }
+               }
+               if (h==(int)(calagedatem+12*cpt)){
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   strcat(optionfilehtmcov,"-cov.htm");
+                   /*fprintf(ficrespop," %.3f", kk1);
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+               }
-   }
+             }
-   else{
+             for(i=1; i<=nlstate;i++){
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+               kk1=0.;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+                 for(j=1; j<=nlstate;j++){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+                 }
-   }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
-   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\
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
- \n\
+           }
- <hr  size=\"2\" color=\"#EC5E5E\">\
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  <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",\
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           fileres,fileres,\
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+           nhstepm = nhstepm/hstepm;
-   fflush(fichtm);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   strcpy(pathr,path);
+           oldm=oldms;savm=savms;
-   strcat(pathr,optionfilefiname);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-      and prints on file fileres'p'. */
+             }
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   fprintf(fichtm,"\n");
+               for(i=1; i<=nlstate;i++) {
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
- 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",\
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-           imx,agemin,agemax,jmin,jmax,jmean);
+             }
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           }
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     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]
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-      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) */
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+     free_vector(popeffectif,0,AGESUP);
+     free_vector(popcount,0,AGESUP);
-   if (mle==-3){
+   }
-     ximort=matrix(1,NDIM,1,NDIM);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     cens=ivector(1,n);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     ageexmed=vector(1,n);
+   fclose(ficrespop);
-     agecens=vector(1,n);
+ } /* End of popforecast */
-     dcwave=ivector(1,n);
+ int fileappend(FILE *fichier, char *optionfich)
-     for (i=1; i<=imx; i++){
+ {
-       dcwave[i]=-1;
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-       for (m=firstpass; m<=lastpass; m++)
+     printf("Problem with file: %s\n", optionfich);
-         if (s[m][i]>nlstate) {
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-           dcwave[i]=m;
+     return (0);
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+   }
-           break;
+   fflush(fichier);
-         }
+   return (1);
-     }
+ }
-     for (i=1; i<=imx; i++) {
-       if (wav[i]>0){
+ /**************** function prwizard **********************/
-         ageexmed[i]=agev[mw[1][i]][i];
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-         j=wav[i];
+ {
-         agecens[i]=1.;
+   /* Wizard to print covariance matrix template */
-         if (ageexmed[i]> 1 && wav[i] > 0){
-           agecens[i]=agev[mw[j][i]][i];
+   char ca[32], cb[32];
-           cens[i]= 1;
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-         }else if (ageexmed[i]< 1)
+   int numlinepar;
-           cens[i]= -1;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-           cens[i]=0 ;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-       }
+   for(i=1; i <=nlstate; i++){
-       else cens[i]=-1;
+     jj=0;
-     }
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
-     for (i=1;i<=NDIM;i++) {
+       jj++;
-       for (j=1;j<=NDIM;j++)
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+       printf("%1d%1d",i,j);
-     }
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
-     p[1]=0.0268; p[NDIM]=0.083;
+         /*        printf(" %lf",param[i][j][k]); */
-     /*printf("%lf %lf", p[1], p[2]);*/
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
+         fprintf(ficparo," 0.");
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+       }
-     strcpy(filerespow,"pow-mort");
+       printf("\n");
-     strcat(filerespow,fileres);
+       fprintf(ficparo,"\n");
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     }
-       printf("Problem with resultfile: %s\n", filerespow);
+   }
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   printf("# Scales (for hessian or gradient estimation)\n");
-     }
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     /*  for (i=1;i<=nlstate;i++)
+   for(i=1; i <=nlstate; i++){
-         for(j=1;j<=nlstate+ndeath;j++)
+     jj=0;
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     for(j=1; j <=nlstate+ndeath; j++){
-     */
+       if(j==i) continue;
-     fprintf(ficrespow,"\n");
+       jj++;
+       fprintf(ficparo,"%1d%1d",i,j);
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+       printf("%1d%1d",i,j);
-     fclose(ficrespow);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-     for(i=1; i <=NDIM; i++)
+         printf(" 0.");
-       for(j=i+1;j<=NDIM;j++)
+         fprintf(ficparo," 0.");
-         matcov[i][j]=matcov[j][i];
+       }
+       numlinepar++;
-     printf("\nCovariance matrix\n ");
+       printf("\n");
-     for(i=1; i <=NDIM; i++) {
+       fprintf(ficparo,"\n");
-       for(j=1;j<=NDIM;j++){
+     }
-         printf("%f ",matcov[i][j]);
+   }
-       }
+   printf("# Covariance matrix\n");
-       printf("\n ");
+ /* # 121 Var(a12)\n\ */
-     }
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-     for (i=1;i<=NDIM;i++)
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ /* # 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\ */
-     lsurv=vector(1,AGESUP);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-     lpop=vector(1,AGESUP);
+   fflush(stdout);
-     tpop=vector(1,AGESUP);
+   fprintf(ficparo,"# Covariance matrix\n");
-     lsurv[agegomp]=100000;
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     for (k=agegomp;k<=AGESUP;k++) {
+   /* #   ...\n\ */
-       agemortsup=k;
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     }
+   for(itimes=1;itimes<=2;itimes++){
+     jj=0;
-     for (k=agegomp;k<agemortsup;k++)
+     for(i=1; i <=nlstate; i++){
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
-     for (k=agegomp;k<agemortsup;k++){
+         for(k=1; k<=ncovmodel;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+           jj++;
-       sumlpop=sumlpop+lpop[k];
+           ca[0]= k+'a'-1;ca[1]='\0';
-     }
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
-     tpop[agegomp]=sumlpop;
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-     for (k=agegomp;k<(agemortsup-3);k++){
+           }else{
-       /*  tpop[k+1]=2;*/
+             printf("%1d%1d%d",i,j,k);
-       tpop[k+1]=tpop[k]-lpop[k];
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-     }
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+           for(li=1;li <=nlstate; li++){
-     for (k=agegomp;k<(agemortsup-2);k++)
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-       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]);
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+                 if(ll<=jj){
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                     if(itimes==1){
-                      stepm, weightopt,\
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                      model,imx,p,matcov,agemortsup);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
-     free_vector(lsurv,1,AGESUP);
+                       printf(" 0.");
-     free_vector(lpop,1,AGESUP);
+                       fprintf(ficparo," 0.");
-     free_vector(tpop,1,AGESUP);
+                     }
-   } /* Endof if mle==-3 */
+                   }else{
+                     if(itimes==1){
-   else{ /* For mle >=1 */
+                       printf(" Var(%s%1d%1d)",ca,i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+                     }else{
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+                       printf(" 0.");
-     for (k=1; k<=npar;k++)
+                       fprintf(ficparo," 0.");
-       printf(" %d %8.5f",k,p[k]);
+                     }
-     printf("\n");
+                   }
-     globpr=1; /* to print the contributions */
+                 }
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+               } /* end lk */
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+             } /* end lj */
-     for (k=1; k<=npar;k++)
+           } /* end li */
-       printf(" %d %8.5f",k,p[k]);
+           printf("\n");
-     printf("\n");
+           fprintf(ficparo,"\n");
-     if(mle>=1){ /* Could be 1 or 2 */
+           numlinepar++;
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+         } /* end k*/
-     }
+       } /*end j */
+     } /* end i */
-     /*--------- results files --------------*/
+   } /* end itimes */
-     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);
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ double gompertz(double x[])
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ {
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   double A,B,L=0.0,sump=0.,num=0.;
-     for(i=1,jk=1; i <=nlstate; i++){
+   int i,n=0; /* n is the size of the sample */
-       for(k=1; k <=(nlstate+ndeath); k++){
-         if (k != i) {
+   for (i=0;i<=imx-1 ; i++) {
-           printf("%d%d ",i,k);
+     sump=sump+weight[i];
-           fprintf(ficlog,"%d%d ",i,k);
+     /*    sump=sump+1;*/
-           fprintf(ficres,"%1d%1d ",i,k);
+     num=num+1;
-           for(j=1; j <=ncovmodel; j++){
+   }
-             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
-             fprintf(ficres,"%lf ",p[jk]);
+   /* for (i=0; i<=imx; i++)
-             jk++;
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-           }
-           printf("\n");
+   for (i=1;i<=imx ; i++)
-           fprintf(ficlog,"\n");
+     {
-           fprintf(ficres,"\n");
+       if (cens[i] == 1 && wav[i]>1)
-         }
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-       }
-     }
+       if (cens[i] == 0 && wav[i]>1)
-     if(mle!=0){
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-       /* Computing hessian and covariance matrix */
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-       ftolhess=ftol; /* Usually correct */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     }
+       if (wav[i] > 1 ) { /* ??? */
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+         L=L+A*weight[i];
-     printf("# Scales (for hessian or gradient estimation)\n");
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-     fprintf(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) {
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-           fprintf(ficres,"%1d%1d",i,j);
-           printf("%1d%1d",i,j);
+   return -2*L*num/sump;
-           fprintf(ficlog,"%1d%1d",i,j);
+ }
-           for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
+ #ifdef GSL
-             fprintf(ficlog," %.5e",delti[jk]);
+ /******************* Gompertz_f Likelihood ******************************/
-             fprintf(ficres," %.5e",delti[jk]);
+ double gompertz_f(const gsl_vector *v, void *params)
-             jk++;
+ {
-           }
+   double A,B,LL=0.0,sump=0.,num=0.;
-           printf("\n");
+   double *x= (double *) v->data;
-           fprintf(ficlog,"\n");
+   int i,n=0; /* n is the size of the sample */
-           fprintf(ficres,"\n");
-         }
+   for (i=0;i<=imx-1 ; i++) {
-       }
+     sump=sump+weight[i];
-     }
+     /*    sump=sump+1;*/
+     num=num+1;
-     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");
+   /* for (i=0; i<=imx; i++)
-     /* # 121 Var(a12)\n\ */
+      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]);*/
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   for (i=1;i<=imx ; i++)
-     /* # 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\ */
+       if (cens[i] == 1 && wav[i]>1)
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-     /* # 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" */
+       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);
-     /* Just to have a covariance matrix which will be more understandable
-        even is we still don't want to manage dictionary of variables
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     */
+       if (wav[i] > 1 ) { /* ??? */
-     for(itimes=1;itimes<=2;itimes++){
+         LL=LL+A*weight[i];
-       jj=0;
+         /*      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]);*/
-       for(i=1; i <=nlstate; i++){
+       }
-         for(j=1; j <=nlstate+ndeath; j++){
+     }
-           if(j==i) continue;
-           for(k=1; k<=ncovmodel;k++){
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-             jj++;
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-             ca[0]= k+'a'-1;ca[1]='\0';
-             if(itimes==1){
+   return -2*LL*num/sump;
-               if(mle>=1)
+ }
-                 printf("#%1d%1d%d",i,j,k);
+ #endif
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+ /******************* Printing html file ***********/
-             }else{
+ void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
-               if(mle>=1)
+                   int lastpass, int stepm, int weightopt, char model[],\
-                 printf("%1d%1d%d",i,j,k);
+                   int imx,  double p[],double **matcov,double agemortsup){
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+   int i,k;
-               fprintf(ficres,"%1d%1d%d",i,j,k);
-             }
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-             ll=0;
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-             for(li=1;li <=nlstate; li++){
+   for (i=1;i<=2;i++)
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+     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]));
-                 if(lj==li) continue;
+   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
-                 for(lk=1;lk<=ncovmodel;lk++){
+   fprintf(fichtm,"</ul>");
-                   ll++;
-                   if(ll<=jj){
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-                     cb[0]= lk +'a'-1;cb[1]='\0';
-                     if(ll<jj){
+  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>");
-                       if(itimes==1){
-                         if(mle>=1)
+  for (k=agegomp;k<(agemortsup-2);k++)
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-                         fprintf(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{
+   fflush(fichtm);
-                         if(mle>=1)
+ }
-                           printf(" %.5e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+ /******************* Gnuplot file **************/
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-                       }
-                     }else{
+   char dirfileres[132],optfileres[132];
-                       if(itimes==1){
-                         if(mle>=1)
+   int ng;
-                           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);
+   /*#ifdef windows */
-                       }else{
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-                         if(mle>=1)
+     /*#endif */
-                           printf(" %.5e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   strcpy(dirfileres,optionfilefiname);
-                       }
+   strcpy(optfileres,"vpl");
-                     }
+   fprintf(ficgp,"set out \"graphmort.svg\"\n ");
-                   }
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-                 } /* end lk */
+   fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
-               } /* end lj */
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-             } /* end li */
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-             if(mle>=1)
-               printf("\n");
+ }
-             fprintf(ficlog,"\n");
-             fprintf(ficres,"\n");
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-             numlinepar++;
+ {
-           } /* end k*/
-         } /*end j */
+   /*-------- data file ----------*/
-       } /* end i */
+   FILE *fic;
-     } /* end itimes */
+   char dummy[]="                         ";
+   int i=0, j=0, n=0;
-     fflush(ficlog);
+   int linei, month, year,iout;
-     fflush(ficres);
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[MAXLINE], strb[MAXLINE];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   char *stratrunc;
-       ungetc(c,ficpar);
+   int lstra;
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
-       fputs(line,ficparo);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     }
+     printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
-     ungetc(c,ficpar);
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
+   }
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+   i=1;
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+   linei=0;
-     if (fage <= 2) {
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       bage = ageminpar;
+     linei=linei+1;
-       fage = agemaxpar;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     }
+       if(line[j] == '\t')
+         line[j] = ' ';
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     }
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       ;
+     };
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     line[j+1]=0;  /* Trims blanks at end of line */
-       ungetc(c,ficpar);
+     if(line[0]=='#'){
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"Comment line\n%s\n",line);
-       puts(line);
+       printf("Comment line\n%s\n",line);
-       fputs(line,ficparo);
+       continue;
      }
-     ungetc(c,ficpar);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     strcpy(line, linetmp);
-     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);
+     for (j=maxwav;j>=1;j--){
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       cutv(stra, strb, line, ' ');
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       }else{
-       ungetc(c,ficpar);
+         errno=0;
-       fgets(line, MAXLINE, ficpar);
+         lval=strtol(strb,&endptr,10);
-       puts(line);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       fputs(line,ficparo);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     }
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-     ungetc(c,ficpar);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           return 1;
+         }
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+       }
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+       s[j][i]=lval;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+       strcpy(line,stra);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+       cutv(stra, strb,line,' ');
-     fprintf(ficres,"pop_based=%d\n",popbased);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+       }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-       ungetc(c,ficpar);
+         month=99;
-       fgets(line, MAXLINE, ficpar);
+         year=9999;
-       puts(line);
+       }else{
-       fputs(line,ficparo);
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     }
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
-     ungetc(c,ficpar);
+         return 1;
+       }
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+       anint[j][i]= (double) year;
-     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);
+       mint[j][i]= (double)month;
-     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);
+       strcpy(line,stra);
-     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);
+     } /* ENd Waves */
-     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.*/
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+     }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+       month=99;
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       year=9999;
+     }else{
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+       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);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+         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;
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     }
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+     andc[i]=(double) year;
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
-    /*------------ free_vector  -------------*/
-    /*  chdir(path); */
+     cutv(stra, strb,line,' ');
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-     free_ivector(wav,1,imx);
+     }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+       month=99;
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+       year=9999;
-     free_lvector(num,1,n);
+     }else{
-     free_vector(agedc,1,n);
+       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);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+       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);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+         return 1;
-     fclose(ficparo);
+     }
-     fclose(ficres);
+     if (year==9999) {
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+         return 1;
-     strcpy(filerespl,"pl");
+     }
-     strcat(filerespl,fileres);
+     annais[i]=(double)(year);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     moisnais[i]=(double)(month);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     strcpy(line,stra);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     }
+     cutv(stra, strb,line,' ');
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     errno=0;
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     dval=strtod(strb,&endptr);
-     pstamp(ficrespl);
+     if( strb[0]=='\0' || (*endptr != '\0')){
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-     fprintf(ficrespl,"#Age ");
+       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);
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+       fflush(ficlog);
-     fprintf(ficrespl,"\n");
+       return 1;
+     }
-     prlim=matrix(1,nlstate,1,nlstate);
+     weight[i]=dval;
+     strcpy(line,stra);
-     agebase=ageminpar;
-     agelim=agemaxpar;
+     for (j=ncovcol;j>=1;j--){
-     ftolpl=1.e-10;
+       cutv(stra, strb,line,' ');
-     i1=cptcoveff;
+       if(strb[0]=='.') { /* Missing status */
-     if (cptcovn < 1){i1=1;}
+         lval=-1;
+       }else{
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         errno=0;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         lval=strtol(strb,&endptr,10);
-         k=k+1;
+         if( strb[0]=='\0' || (*endptr != '\0')){
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-         fprintf(ficrespl,"\n#******");
+           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);
-         printf("\n#******");
+           return 1;
-         fprintf(ficlog,"\n#******");
+         }
-         for(j=1;j<=cptcoveff;j++) {
+       }
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       if(lval <-1 || lval >1){
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficrespl,"******\n");
+  For example, for multinomial values like 1, 2 and 3,\n \
-         printf("******\n");
+  build V1=0 V2=0 for the reference value (1),\n \
-         fprintf(ficlog,"******\n");
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-         for (age=agebase; age<=agelim; age++){
+  output of IMaCh is often meaningless.\n \
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+  Exiting.\n",lval,linei, i,line,j);
-           fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-           for(j=1;j<=cptcoveff;j++)
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-           for(i=1; i<=nlstate;i++)
+  For example, for multinomial values like 1, 2 and 3,\n \
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+  build V1=0 V2=0 for the reference value (1),\n \
-           fprintf(ficrespl,"\n");
+         V1=1 V2=0 for (2) \n \
-         }
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       }
+  output of IMaCh is often meaningless.\n \
-     }
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-     fclose(ficrespl);
+         return 1;
+       }
-     /*------------- h Pij x at various ages ------------*/
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     }
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     lstra=strlen(stra);
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-     }
+       stratrunc = &(stra[lstra-9]);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+       num[i]=atol(stratrunc);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     }
+     else
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+       num[i]=atol(stra);
-     /*if (stepm<=24) stepsize=2;*/
+     /*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;}*/
-     agelim=AGESUP;
-     hstepm=stepsize*YEARM; /* Every year of age */
+     i=i+1;
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   } /* End loop reading  data */
-     /* hstepm=1;   aff par mois*/
+   *imax=i-1; /* Number of individuals */
-     pstamp(ficrespij);
+   fclose(fic);
-     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++){
+   return (0);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   /* endread: */
-         k=k+1;
+     printf("Exiting readdata: ");
-         fprintf(ficrespij,"\n#****** ");
+     fclose(fic);
-         for(j=1;j<=cptcoveff;j++)
+     return (1);
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrespij,"******\n");
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+ }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ void removespace(char *str) {
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   char *p1 = str, *p2 = str;
+   do
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+     while (*p2 == ' ')
+       p2++;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   while (*p1++ == *p2++);
-           oldm=oldms;savm=savms;
+ }
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-           for(i=1; i<=nlstate;i++)
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
-             for(j=1; j<=nlstate+ndeath;j++)
+    * - nagesqr = 1 if age*age in the model, otherwise 0.
-               fprintf(ficrespij," %1d-%1d",i,j);
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
-           fprintf(ficrespij,"\n");
+    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
-           for (h=0; h<=nhstepm; h++){
+    * - cptcovage number of covariates with age*products =2
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+    * - cptcovs number of simple covariates
-             for(i=1; i<=nlstate;i++)
+    * - 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
-               for(j=1; j<=nlstate+ndeath;j++)
+    *     which is a new column after the 9 (ncovcol) variables.
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-             fprintf(ficrespij,"\n");
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-           }
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-           fprintf(ficrespij,"\n");
+  */
-         }
+ {
-       }
+   int i, j, k, ks;
-     }
+   int  j1, k1, k2;
+   char modelsav[80];
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char *strpt;
-     fclose(ficrespij);
+   /*removespace(model);*/
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-     for(i=1;i<=AGESUP;i++)
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-       for(j=1;j<=NCOVMAX;j++)
+     if (strstr(model,"AGE") !=0){
-         for(k=1;k<=NCOVMAX;k++)
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
-           probs[i][j][k]=0.;
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
+       return 1;
-     /*---------- Forecasting ------------------*/
+     }
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if (strstr(model,"v") !=0){
-     if(prevfcast==1){
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-       /*    if(stepm ==1){*/
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       return 1;
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     }
-       /*      }  */
+     strcpy(modelsav,model);
-       /*      else{ */
+     if ((strpt=strstr(model,"age*age")) !=0){
-       /*        erreur=108; */
+       printf(" strpt=%s, model=%s\n",strpt, model);
-       /*        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); */
+       if(strpt != 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); */
+       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-       /*      } */
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     }
+  corresponding column of parameters.\n",model);
+       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     /*---------- Health expectancies and variances ------------*/
+  corresponding column of parameters.\n",model); fflush(ficlog);
+       return 1;
-     strcpy(filerest,"t");
+     }
-     strcat(filerest,fileres);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+       nagesqr=1;
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       if (strstr(model,"+age*age") !=0)
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+         substrchaine(modelsav, model, "+age*age");
-     }
+       else if (strstr(model,"age*age+") !=0)
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+         substrchaine(modelsav, model, "age*age+");
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       else
+         substrchaine(modelsav, model, "age*age");
+     }else
-     strcpy(filerese,"e");
+       nagesqr=0;
-     strcat(filerese,fileres);
+     if (strlen(modelsav) >1){
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
-     }
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+                    * cst, age and age*age
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
+                   /* including age products which are counted in cptcovage.
-     strcpy(fileresstde,"stde");
+                   * but the covariates which are products must be treated
-     strcat(fileresstde,fileres);
+                   * separately: ncovn=4- 2=2 (V1+V3). */
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-       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);
+       /*   Design
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+        *  <          ncovcol=8                >
-     strcpy(filerescve,"cve");
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-     strcat(filerescve,fileres);
+        *   k=  1    2      3       4     5       6      7        8
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+        *  covar[k,i], value of kth covariate if not including age for individual i:
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+        *       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
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+        *  Tage[++cptcovage]=k
+        *       if products, new covar are created after ncovcol with k1
-     strcpy(fileresv,"v");
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-     strcat(fileresv,fileres);
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+        *  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
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-     }
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+        *  <          ncovcol=8                >
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-     /*  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",\
+        * p Tprod[1]@2={                         6, 5}
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
-     */
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     if (mobilav!=0) {
+        *How to reorganize?
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+        * Struct []
-       }
+        */
-     }
+       /* This loop fills the array Tvar from the string 'model'.*/
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-         k=k+1;
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-         fprintf(ficrest,"\n#****** ");
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
-         for(j=1;j<=cptcoveff;j++)
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       /*        k=1 Tvar[1]=2 (from V2) */
-         fprintf(ficrest,"******\n");
+       /*        k=5 Tvar[5] */
+       /* for (k=1; k<=cptcovn;k++) { */
-         fprintf(ficreseij,"\n#****** ");
+       /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-         fprintf(ficresstdeij,"\n#****** ");
+       /*        } */
-         fprintf(ficrescveij,"\n#****** ");
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
-         for(j=1;j<=cptcoveff;j++) {
+       /*
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         Tvar[k]=0;
-         }
+       cptcovage=0;
-         fprintf(ficreseij,"******\n");
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-         fprintf(ficresstdeij,"******\n");
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-         fprintf(ficrescveij,"******\n");
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-         fprintf(ficresvij,"\n#****** ");
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-         for(j=1;j<=cptcoveff;j++)
+         /*scanf("%d",i);*/
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-         fprintf(ficresvij,"******\n");
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+             /* covar is not filled and then is empty */
-         oldm=oldms;savm=savms;
+             cptcovprod--;
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-         oldm=oldms;savm=savms;
+             /*printf("stre=%s ", stre);*/
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-         if(popbased==1){
+             cptcovprod--;
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+             cutl(stre,strb,strc,'V');
-         }
+             Tvar[k]=atoi(stre);
+             cptcovage++;
-         pstamp(ficrest);
+             Tage[cptcovage]=k;
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-         fprintf(ficrest,"\n");
+             cptcovn++;
+             cptcovprodnoage++;k1++;
-         epj=vector(1,nlstate+1);
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-         for(age=bage; age <=fage ;age++){
+             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+                                    because this model-covariate is a construction we invent a new column
-           if (popbased==1) {
+                                    ncovcol + k1
-             if(mobilav ==0){
+                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-               for(i=1; i<=nlstate;i++)
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-                 prlim[i][i]=probs[(int)age][i][k];
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-             }else{ /* mobilav */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-               for(i=1; i<=nlstate;i++)
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-             }
+             k2=k2+2;
-           }
+             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-           fprintf(ficrest," %4.0f",age);
+             for (i=1; i<=lastobs;i++){
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               /* Computes the new covariate which is a product of
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+             }
-             }
+           } /* End age is not in the model */
-             epj[nlstate+1] +=epj[j];
+         } /* End if model includes a product */
-           }
+         else { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-           for(i=1, vepp=0.;i <=nlstate;i++)
+           /*  scanf("%d",i);*/
-             for(j=1;j <=nlstate;j++)
+           cutl(strd,strc,strb,'V');
-               vepp += vareij[i][j][(int)age];
+           ks++; /**< Number of simple covariates */
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           cptcovn++;
-           for(j=1;j <=nlstate;j++){
+           Tvar[k]=atoi(strd);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+         }
-           }
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-           fprintf(ficrest,"\n");
+         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-         }
+           scanf("%d",i);*/
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       } /* end of loop + on total covariates */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     } /* end if strlen(modelsave == 0) age*age might exist */
-         free_vector(epj,1,nlstate+1);
+   } /* end if strlen(model == 0) */
-       }
-     }
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     free_vector(weight,1,n);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-     free_imatrix(Tvard,1,15,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-     free_matrix(anint,1,maxwav,1,n);
+   printf("cptcovprod=%d ", cptcovprod);
-     free_matrix(mint,1,maxwav,1,n);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-     free_ivector(cod,1,n);
-     free_ivector(tab,1,NCOVMAX);
+   scanf("%d ",i);*/
-     fclose(ficreseij);
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-     fclose(ficresvij);
+   /*endread:*/
-     fclose(ficrest);
+     printf("Exiting decodemodel: ");
-     fclose(ficpar);
+     return (1);
+ }
-     /*------- Variance of period (stable) prevalence------*/
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-     strcpy(fileresvpl,"vpl");
+ {
-     strcat(fileresvpl,fileres);
+   int i, m;
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+   for (i=1; i<=imx; i++) {
-       exit(0);
+     for(m=2; (m<= maxwav); m++) {
-     }
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+         anint[m][i]=9999;
+         s[m][i]=-1;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       }
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         k=k+1;
+         *nberr = *nberr + 1;
-         fprintf(ficresvpl,"\n#****** ");
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
-         for(j=1;j<=cptcoveff;j++)
+         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);
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         s[m][i]=-1;
-         fprintf(ficresvpl,"******\n");
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         (*nberr)++;
-         oldm=oldms;savm=savms;
+         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]);
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         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]);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
+   }
-     fclose(ficresvpl);
+   for (i=1; i<=imx; i++)  {
-     /*---------- End : free ----------------*/
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(m=firstpass; (m<= lastpass); m++){
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         if (s[m][i] >= nlstate+1) {
-   }  /* mle==-3 arrives here for freeing */
+           if(agedc[i]>0){
-   free_matrix(prlim,1,nlstate,1,nlstate);
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+               agev[m][i]=agedc[i];
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+             }else {
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+               if ((int)andc[i]!=9999){
-     free_matrix(covar,0,NCOVMAX,1,n);
+                 nbwarn++;
-     free_matrix(matcov,1,npar,1,npar);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-     /*free_vector(delti,1,npar);*/
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+                 agev[m][i]=-1;
-     free_matrix(agev,1,maxwav,1,imx);
+               }
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+             }
+           } /* agedc > 0 */
-     free_ivector(ncodemax,1,8);
+         }
-     free_ivector(Tvar,1,15);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-     free_ivector(Tprod,1,15);
+                                  years but with the precision of a month */
-     free_ivector(Tvaraff,1,15);
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-     free_ivector(Tage,1,15);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-     free_ivector(Tcode,1,100);
+             agev[m][i]=1;
+           else if(agev[m][i] < *agemin){
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+             *agemin=agev[m][i];
-     free_imatrix(codtab,1,100,1,10);
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-   fflush(fichtm);
+           }
-   fflush(ficgp);
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-   if((nberr >0) || (nbwarn>0)){
+           }
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+           /*     agev[m][i] = age[i]+2*m;*/
-   }else{
+         }
-     printf("End of Imach\n");
+         else { /* =9 */
-     fprintf(ficlog,"End of Imach\n");
+           agev[m][i]=1;
-   }
+           s[m][i]=-1;
-   printf("See log file on %s\n",filelog);
+         }
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+       }
-   (void) gettimeofday(&end_time,&tzp);
+       else /*= 0 Unknown */
-   tm = *localtime(&end_time.tv_sec);
+         agev[m][i]=1;
-   tmg = *gmtime(&end_time.tv_sec);
+     }
-   strcpy(strtend,asctime(&tm));
-   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);
+   for (i=1; i<=imx; i++)  {
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+         (*nberr)++;
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+         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,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+         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);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+         return 1;
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+       }
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     }
-   fclose(fichtm);
+   }
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
-   fclose(fichtmcov);
+   /*for (i=1; i<=imx; i++){
-   fclose(ficgp);
+   for (m=firstpass; (m<lastpass); m++){
-   fclose(ficlog);
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-   /*------ End -----------*/
+ }
+ }*/
-    printf("Before Current directory %s!\n",pathcd);
-    if(chdir(pathcd) != 0)
-     printf("Can't move to directory %s!\n",path);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-   if(getcwd(pathcd,MAXLINE) > 0)
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     printf("Current directory %s!\n",pathcd);
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+   return (0);
-   sprintf(plotcmd,"gnuplot");
+  /* endread:*/
- #ifndef UNIX
+     printf("Exiting calandcheckages: ");
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+     return (1);
- #endif
+ }
-   if(!stat(plotcmd,&info)){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ #if defined(_MSC_VER)
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     }else
+ //#include "stdafx.h"
-       strcpy(pplotcmd,plotcmd);
+ //#include <stdio.h>
- #ifdef UNIX
+ //#include <tchar.h>
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+ //#include <windows.h>
-     if(!stat(plotcmd,&info)){
+ //#include <iostream>
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
-     }else
-       strcpy(pplotcmd,plotcmd);
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
- #endif
-   }else
+ BOOL IsWow64()
-     strcpy(pplotcmd,plotcmd);
+ {
+         BOOL bIsWow64 = FALSE;
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
+         //  (HANDLE, PBOOL);
-   if((outcmd=system(plotcmd)) != 0){
-     printf("\n Problem with gnuplot\n");
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
-   }
-   printf(" Wait...");
+         HMODULE module = GetModuleHandle(_T("kernel32"));
-   while (z[0] != 'q') {
+         const char funcName[] = "IsWow64Process";
-     /* chdir(path); */
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+                 GetProcAddress(module, funcName);
-     scanf("%s",z);
- /*     if (z[0] == 'c') system("./imach"); */
+         if (NULL != fnIsWow64Process)
-     if (z[0] == 'e') {
+         {
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+                 if (!fnIsWow64Process(GetCurrentProcess(),
-       system(optionfilehtm);
+                         &bIsWow64))
-     }
+                         //throw std::exception("Unknown error");
-     else if (z[0] == 'g') system(plotcmd);
+                         printf("Unknown error\n");
-     else if (z[0] == 'q') exit(0);
+         }
-   }
+         return bIsWow64 != FALSE;
-   end:
+ }
-   while (z[0] != 'q') {
+ #endif
-     printf("\nType  q for exiting: ");
-     scanf("%s",z);
+ void syscompilerinfo(int logged)
-   }
+  {
- }
+    /* #include "syscompilerinfo.h"*/
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
+ #endif
+ #include <stdint.h>
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+ #endif
+ #if defined(_MSC_VER)
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+ #endif
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
+    printf(" for "); if (logged) fprintf(ficlog, " for ");
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
+     // Windows (x64 and x86)
+    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
+ #elif __unix__ // all unices, not all compilers
+     // Unix
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
+ #elif __linux__
+     // linux
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
+ #elif __APPLE__
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
+ #endif
+ /*  __MINGW32__   */
+ /*  __CYGWIN__   */
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
+ /* _WIN64  // Defined for applications for Win64. */
+ /* _M_X64 // Defined for compilations that target x64 processors. */
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
+ #if UINTPTR_MAX == 0xffffffff
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
+ #endif
+ #if defined(__GNUC__)
+ # if defined(__GNUC_PATCHLEVEL__)
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100)
+ # endif
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+    if (uname(&sysInfo) != -1) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+ #endif
+    //   void main()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+  }
+  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   int i, j, k, i1 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(filerespl,"PL_");
+   strcat(filerespl,fileresu);
+   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   fprintf(ficrespl,"\n");
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+     agebase=ageminpar;
+     agelim=agemaxpar;
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         /* to clean */
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+         fprintf(ficrespl,"#******");
+         printf("#******");
+         fprintf(ficlog,"#******");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         fprintf(ficrespl,"#Age ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+         fprintf(ficrespl,"Total Years_to_converge\n");
+         for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
+           fprintf(ficrespl,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           tot=0.;
+           for(i=1; i<=nlstate;i++){
+             tot +=  prlim[i][i];
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           }
+           fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
+         } /* Age */
+         /* was end of cptcod */
+     } /* cptcov */
+         return 0;
+ }
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k;
+   double agedeb;
+   double ***p3mat;
+     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     i1= pow(2,cptcoveff);
+    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+    /*   k=k+1;  */
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespij,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
+       /*}*/
+     }
+         return 0;
+ }
+ /***********************************************/
+ /**************** Main Program *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
+   int status = GSL_SUCCESS;
+   double ssval;
+ #endif
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int ncvyearnp=0;
+   int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
+   int jj, ll, li, lj, lk;
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int num_filled;
+   int itimes;
+   int NDIM=2;
+   int vpopbased=0;
+   char ca[32], cb[32];
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
+   double agedeb=0.;
+   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
+   double fret;
+   double dum=0.; /* Dummy variable */
+   double ***p3mat;
+   double ***mobaverage;
+   char line[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+   char model[MAXLINE], modeltemp[MAXLINE];
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10;
+   int c,  h , cpt, c2;
+   int jl=0;
+   int i1, j1, jk, stepsize=0;
+   int count=0;
+   int *tab;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   int mobilav=0,popforecast=0;
+   int hstepm=0, nhstepm=0;
+   int agemortsup;
+   float  sumlpop=0.;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   double bage=0, fage=110., age, agelim=0., agebase=0.;
+   double ftolpl=FTOL;
+   double **prlim;
+   double ***param; /* Matrix of parameters */
+   double  *p;
+   double **matcov; /* Matrix of covariance */
+   double **hess; /* Hessian matrix */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+   int *dcwave;
+   char z[1]="c";
+   /*char  *strt;*/
+   char strtend[80];
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
+   /*tml = *localtime(&start_time.tm_sec);*/
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
+   getcwd(pathcd, size);
+ #endif
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
+     if(!fgets(pathr,FILENAMELENGTH,stdin)){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
+     i=strlen(pathr);
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+     }
+     i=strlen(pathr);
+     if( i==0 ){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
+     }
+   }
+   else{
+     strcpy(pathtot,argv[1]);
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   /*cygwin_split_path(pathtot,path,optionfile);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #ifdef WIN32
+   _chdir(path); /* Can be a relative path */
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ #else
+   chdir(path); /* Can be a relative path */
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
+ #endif
+   printf("Current directory %s!\n",pathcd);
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
+   /*-------- arguments in the command line --------*/
+   /* Main Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   syscompilerinfo(1);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
+   /* */
+   strcpy(fileres,"r");
+   strcat(fileres, optionfilefiname);
+   strcat(fileresu, optionfilefiname); /* Without r in front */
+   strcat(fileres,".txt");    /* Other files have txt extension */
+   strcat(fileresu,".txt");    /* Other files have txt extension */
+   /* Main ---------arguments file --------*/
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fflush(ficlog);
+     /* goto end; */
+     exit(70);
+   }
+   strcpy(filereso,"o");
+   strcat(filereso,fileresu);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
+     goto end;
+   }
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
+     /* First parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+     if (num_filled != 5) {
+       printf("Should be 5 parameters\n");
+     }
+     numlinepar++;
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+   }
+   /* Second parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+     if (num_filled != 8) {
+       printf("Not 8\n");
+     }
+     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+   /* Third parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled == 0)
+             model[0]='\0';
+     else if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     }
+     else{
+       if (model[0]=='+'){
+         for(i=1; i<=strlen(model);i++)
+           modeltemp[i-1]=model[i];
+         strcpy(model,modeltemp);
+       }
+     }
+     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     printf("model=1+age+%s\n",model);fflush(stdout);
+   }
+   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+   /* numlinepar=numlinepar+3; /\* In general *\/ */
+   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fflush(ficlog);
+   /* if(model[0]=='#'|| model[0]== '\0'){ */
+   if(model[0]=='#'){
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+     if(mle != -1){
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       exit(1);
+     }
+   }
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
+     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+       z[0]=line[1];
+     }
+     /* printf("****line [1] = %c \n",line[1]); */
+     fputs(line, stdout);
+     //puts(line);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
+   }
+   ungetc(c,ficpar);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
+   */
+   if (strlen(model)>1)
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
+   else
+     ncovmodel=2; /* Constant and age */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
+     goto end;
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
+     fclose (ficlog);
+     goto end;
+     exit(0);
+   }
+   else if(mle==-3) { /* Main Wizard */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     matcov=matrix(1,npar,1,npar);
+     hess=matrix(1,npar,1,npar);
+   }
+   else{
+     /* Read guessed parameters */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
+       j=0;
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) || (j1 != jj)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
+           printf("%1d%1d",i,jj);
+         fprintf(ficlog,"%1d%1d",i,jj);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads scales values */
+     p=param[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ( (i1-i) * (j1-j) != 0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads covariance matrix */
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     hess=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     /* Scans npar lines */
+     for(i=1; i <=npar; i++){
+       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+       if(count != 3){
+         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         exit(1);
+       }else
+       if(mle==1)
+         printf("%1d%1d%1d",i1,j1,jk);
+       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
+       fscanf(ficpar,"\n");
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
+     }
+     /* End of read covariance matrix npar lines */
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
+   /*  Main data
+    */
+   n= lastobs;
+   num=lvector(1,n);
+   moisnais=vector(1,n);
+   annais=vector(1,n);
+   moisdc=vector(1,n);
+   andc=vector(1,n);
+   agedc=vector(1,n);
+   cod=ivector(1,n);
+   weight=vector(1,n);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   mint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
+     goto end;
+   /* Calculation of the number of parameters from char model */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
+ /* Main decodemodel */
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* */
+   wav=ivector(1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* 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],codtabm(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);
+           /**< 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     2
+            *    10     2     1     1     2
+            *    11 i=6 1     2     1     2
+            *    12     2     2     1     2
+            *    13 i=7 1 i=4 1     2     2
+            *    14     2     1     2     2
+            *    15 i=8 1     2     2     2
+            *    16     2     2     2     2
+            */
+   /* /\* for(h=1; h <=100 ;h++){  *\/ */
+   /*   /\* printf("h=%2d ", h); *\/ */
+   /*    /\* for(k=1; k <=10; k++){ *\/ */
+   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
+   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
+   /*    /\* } *\/ */
+   /*    /\* printf("\n"); *\/ */
+   /* } */
+   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
+   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
+   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
+   /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
+   /*      h++; */
+   /*      if (h>m)  */
+   /*        h=1; */
+   /*      codtab[h][k]=j; */
+   /*      /\* codtab[12][3]=1; *\/ */
+   /*      /\*codtab[h][Tvar[k]]=j;*\/ */
+   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
+   /*    }  */
+   /*     } */
+   /*   } */
+   /* }  */
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
+   /* for(i=1; i <=m ;i++){  */
+   /*    for(k=1; k <=cptcovn; k++){ */
+   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
+   /*    } */
+   /*    printf("\n"); */
+   /* } */
+   /*   scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
+   /* Initialisation of ----------- gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-MORT_");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# IMaCh-%s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /* Initialisation of --------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-MORT_");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br>  \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <font size=\"2\">IMaCh-%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+ #ifdef WIN32
+   _chdir(optionfilefiname); /* Move to directory named optionfile */
+ #else
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+ #endif
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /* For mortality only */
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     /*printf("%lf %lf", p[1], p[2]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #else
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"POW-MORT_");
+     strcat(filerespow,fileresu);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #else
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+     /*     gsl_vector_set(x, 0, 0.0268); */
+     /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     fprintf(ficlog,"\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+         fprintf(ficlog,"%f ",matcov[i][j]);
+       }
+       printf("\n ");  fprintf(ficlog,"\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++) {
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     }
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else
+       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 mortality only */
+   /* Standard  */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
+     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+       /* mlikeli uses func not funcone */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     }
+     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle != 0){
+       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
+       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     /*  */
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle >= 1) /* To big for the screen */
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.7e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((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 / */
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileresu,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, ftolpl, ncvyear);
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* ------ Other prevalence ratios------------ */
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"E_");
+     strcat(filerese,fileresu);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \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]][codtabm(k,j)]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"T_");
+     strcat(filerest,fileresu);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"STDE_");
+     strcat(fileresstde,fileresu);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"CVE_");
+     strcat(filerescve,fileresu);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"V_");
+     strcat(fileresv,fileresu);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \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]][codtabm(k,j)]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         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; /* ZZ Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+             /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
+             /* printf(" age %4.0f ",age); */
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+                 /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             /* printf(" age %4.0f \n",age); */
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         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,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \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]][codtabm(k,j)]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     free_matrix(hess,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(ncodemaxwundef,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     /* free_imatrix(codtab,1,100,1,10); */
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+ #ifdef WIN32
+    if (_chdir(pathcd) != 0)
+            printf("Can't move to directory %s!\n",path);
+    if(_getcwd(pathcd,MAXLINE) > 0)
+ #else
+    if(chdir(pathcd) != 0)
+            printf("Can't move to directory %s!\n", path);
+    if (getcwd(pathcd, MAXLINE) > 0)
+ #endif
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: "); fflush(stdout);
+     scanf("%s",z);
+   }
+ }

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