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Diff for /imach/src/imach.c between versions 1.125 and 1.185

-version 1.125, 2006/04/04 15:20:31
+version 1.185, 2015/03/11 13:26:42
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 POWELL /* Instead of NLOPT */
- extern int errno;
+ /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
+ /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
- /* #include <sys/time.h> */
- #include <time.h>
+ #include <math.h>
- #include "timeval.h"
+ #include <stdio.h>
+ #include <stdlib.h>
- /* #include <libintl.h> */
+ #include <string.h>
- /* #define _(String) gettext (String) */
+ #ifdef _WIN32
- #define MAXLINE 256
+ #include <io.h>
+ #include <windows.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <tchar.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #else
- #define FILENAMELENGTH 132
+ #include <unistd.h>
+ #endif
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <limits.h>
+ #include <sys/types.h>
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #if defined(__GNUC__)
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- #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 <sys/stat.h>
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #include <errno.h>
- #define MAXN 20000
+ /* extern int errno; */
- #define YEARM 12. /* Number of months per year */
- #define AGESUP 130
+ /* #ifdef LINUX */
- #define AGEBASE 40
+ /* #include <time.h> */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ /* #include "timeval.h" */
- #ifdef UNIX
+ /* #else */
- #define DIRSEPARATOR '/'
+ /* #include <sys/time.h> */
- #define CHARSEPARATOR "/"
+ /* #endif */
- #define ODIRSEPARATOR '\\'
- #else
+ #include <time.h>
- #define DIRSEPARATOR '\\'
- #define CHARSEPARATOR "\\"
+ #ifdef GSL
- #define ODIRSEPARATOR '/'
+ #include <gsl/gsl_errno.h>
- #endif
+ #include <gsl/gsl_multimin.h>
+ #endif
- /* $Id$ */
- /* $State$ */
+ #ifdef NLOPT
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #include <nlopt.h>
- char fullversion[]="$Revision$ $Date$";
+ typedef struct {
- char strstart[80];
+   double (* function)(double [] );
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ } myfunc_data ;
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ #endif
- int nvar;
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ /* #include <libintl.h> */
- int npar=NPARMAX;
+ /* #define _(String) gettext (String) */
- int nlstate=2; /* Number of live states */
- int ndeath=1; /* Number of dead states */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- int popbased=0;
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define FILENAMELENGTH 132
- int maxwav; /* Maxim number of waves */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int mle, weightopt;
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define NINTERVMAX 8
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- double jmean; /* Mean space between 2 waves */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define MAXN 20000
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define YEARM 12. /**< Number of months per year */
- FILE *ficlog, *ficrespow;
+ #define AGESUP 130
- int globpr; /* Global variable for printing or not */
+ #define AGEBASE 40
- double fretone; /* Only one call to likelihood */
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- long ipmx; /* Number of contributions */
+ #ifdef _WIN32
- double sw; /* Sum of weights */
+ #define DIRSEPARATOR '\\'
- char filerespow[FILENAMELENGTH];
+ #define CHARSEPARATOR "\\"
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #define ODIRSEPARATOR '/'
- FILE *ficresilk;
+ #else
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define DIRSEPARATOR '/'
- FILE *ficresprobmorprev;
+ #define CHARSEPARATOR "/"
- FILE *fichtm, *fichtmcov; /* Html File */
+ #define ODIRSEPARATOR '\\'
- FILE *ficreseij;
+ #endif
- char filerese[FILENAMELENGTH];
- FILE *ficresstdeij;
+ /* $Id$ */
- char fileresstde[FILENAMELENGTH];
+ /* $State$ */
- FILE *ficrescveij;
- char filerescve[FILENAMELENGTH];
+ char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- FILE  *ficresvij;
+ char fullversion[]="$Revision$ $Date$";
- char fileresv[FILENAMELENGTH];
+ char strstart[80];
- FILE  *ficresvpl;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- char fileresvpl[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char title[MAXLINE];
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char command[FILENAMELENGTH];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- int  outcmd=0;
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int cptcov=0; /* Working variable */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int npar=NPARMAX;
- char filerest[FILENAMELENGTH];
+ int nlstate=2; /* Number of live states */
- char fileregp[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
- char popfile[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int popbased=0;
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int *wav; /* Number of waves for this individuual 0 is possible */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int maxwav=0; /* Maxim number of waves */
- struct timezone tzp;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- extern int gettimeofday();
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- long time_value;
+                    to the likelihood and the sum of weights (done by funcone)*/
- extern long time();
+ int mle=1, weightopt=0;
- char strcurr[80], strfor[80];
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- char *endptr;
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- long lval;
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double dval;
+ int countcallfunc=0;  /* Count the number of calls to func */
+ double jmean=1; /* Mean space between 2 waves */
- #define NR_END 1
+ double **matprod2(); /* test */
- #define FREE_ARG char*
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define FTOL 1.0e-10
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ /*FILE *fic ; */ /* Used in readdata only */
- #define NRANSI
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- #define ITMAX 200
+ FILE *ficlog, *ficrespow;
+ int globpr=0; /* Global variable for printing or not */
- #define TOL 2.0e-4
+ double fretone; /* Only one call to likelihood */
+ long ipmx=0; /* Number of contributions */
- #define CGOLD 0.3819660
+ double sw; /* Sum of weights */
- #define ZEPS 1.0e-10
+ char filerespow[FILENAMELENGTH];
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
- #define GOLD 1.618034
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define GLIMIT 100.0
+ FILE *ficresprobmorprev;
- #define TINY 1.0e-20
+ FILE *fichtm, *fichtmcov; /* Html File */
+ FILE *ficreseij;
- static double maxarg1,maxarg2;
+ char filerese[FILENAMELENGTH];
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ FILE *ficresstdeij;
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char filerescve[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- static double sqrarg;
+ FILE  *ficresvpl;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ char fileresvpl[FILENAMELENGTH];
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char title[MAXLINE];
- int agegomp= AGEGOMP;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- int imx;
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- int stepm=1;
+ char command[FILENAMELENGTH];
- /* Stepm, step in month: minimum step interpolation*/
+ int  outcmd=0;
- int estepm;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char filelog[FILENAMELENGTH]; /* Log file */
- int m,nb;
+ char filerest[FILENAMELENGTH];
- long *num;
+ char fileregp[FILENAMELENGTH];
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char popfile[FILENAMELENGTH];
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- double *ageexmed,*agecens;
- double dateintmean=0;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
+ /* struct timezone tzp; */
- double *weight;
+ /* extern int gettimeofday(); */
- int **s; /* Status */
+ struct tm tml, *gmtime(), *localtime();
- double *agedc, **covar, idx;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ extern time_t time();
- double *lsurv, *lpop, *tpop;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- double ftolhess; /* Tolerance for computing hessian */
+ struct tm tm;
- /**************** split *************************/
+ char strcurr[80], strfor[80];
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- {
+ char *endptr;
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ long lval;
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ double dval;
-   */
-   char  *ss;                            /* pointer */
+ #define NR_END 1
-   int   l1, l2;                         /* length counters */
+ #define FREE_ARG char*
+ #define FTOL 1.0e-10
-   l1 = strlen(path );                   /* length of path */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define NRANSI
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define ITMAX 200
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ #define TOL 2.0e-4
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define CGOLD 0.3819660
-     /* get current working directory */
+ #define ZEPS 1.0e-10
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-       return( GLOCK_ERROR_GETCWD );
+ #define GOLD 1.618034
-     }
+ #define GLIMIT 100.0
-     /* got dirc from getcwd*/
+ #define TINY 1.0e-20
-     printf(" DIRC = %s \n",dirc);
-   } else {                              /* strip direcotry from path */
+ static double maxarg1,maxarg2;
-     ss++;                               /* after this, the filename */
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     l2 = strlen( ss );                  /* length of filename */
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-     strcpy( name, ss );         /* save file name */
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ #define rint(a) floor(a+0.5)
-     dirc[l1-l2] = 0;                    /* add zero */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     printf(" DIRC2 = %s \n",dirc);
+ #define mytinydouble 1.0e-16
-   }
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-   /* We add a separator at the end of dirc if not exists */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-   l1 = strlen( dirc );                  /* length of directory */
+ /* static double dsqrarg; */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-     dirc[l1] =  DIRSEPARATOR;
+ static double sqrarg;
-     dirc[l1+1] = 0;
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-     printf(" DIRC3 = %s \n",dirc);
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   }
+ int agegomp= AGEGOMP;
-   ss = strrchr( name, '.' );            /* find last / */
-   if (ss >0){
+ int imx;
-     ss++;
+ int stepm=1;
-     strcpy(ext,ss);                     /* save extension */
+ /* Stepm, step in month: minimum step interpolation*/
-     l1= strlen( name);
-     l2= strlen(ss)+1;
+ int estepm;
-     strncpy( finame, name, l1-l2);
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     finame[l1-l2]= 0;
-   }
+ int m,nb;
+ long *num;
-   return( 0 );                          /* we're done */
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- }
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ double **pmmij, ***probs;
+ double *ageexmed,*agecens;
- /******************************************/
+ double dateintmean=0;
- void replace_back_to_slash(char *s, char*t)
+ double *weight;
- {
+ int **s; /* Status */
-   int i;
+ double *agedc;
-   int lg=0;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   i=0;
+                   * covar=matrix(0,NCOVMAX,1,n);
-   lg=strlen(t);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   for(i=0; i<= lg; i++) {
+ double  idx;
-     (s[i] = t[i]);
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-     if (t[i]== '\\') s[i]='/';
+ int *Ndum; /** Freq of modality (tricode */
-   }
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
- }
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
- int nbocc(char *s, char occ)
- {
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-   int i,j=0;
+ double ftolhess; /**< Tolerance for computing hessian */
-   int lg=20;
-   i=0;
+ /**************** split *************************/
-   lg=strlen(s);
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   for(i=0; i<= lg; i++) {
+ {
-   if  (s[i] == occ ) j++;
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   }
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   return j;
+   */
- }
+   char  *ss;                            /* pointer */
+   int   l1, l2;                         /* length counters */
- void cutv(char *u,char *v, char*t, char occ)
- {
+   l1 = strlen(path );                   /* length of path */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-      gives u="abcedf" and v="ghi2j" */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   int i,lg,j,p=0;
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   i=0;
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   for(j=0; j<=strlen(t)-1; j++) {
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     /* get current working directory */
-   }
+     /*    extern  char* getcwd ( char *buf , int len);*/
+ #ifdef WIN32
-   lg=strlen(t);
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   for(j=0; j<p; j++) {
+ #else
-     (u[j] = t[j]);
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
-   }
+ #endif
-      u[p]='\0';
+       return( GLOCK_ERROR_GETCWD );
+     }
-    for(j=0; j<= lg; j++) {
+     /* got dirc from getcwd*/
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     printf(" DIRC = %s \n",dirc);
-   }
+   } else {                              /* strip direcotry from path */
- }
+     ss++;                               /* after this, the filename */
+     l2 = strlen( ss );                  /* length of filename */
- /********************** nrerror ********************/
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     strcpy( name, ss );         /* save file name */
- void nrerror(char error_text[])
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
- {
+     dirc[l1-l2] = 0;                    /* add zero */
-   fprintf(stderr,"ERREUR ...\n");
+     printf(" DIRC2 = %s \n",dirc);
-   fprintf(stderr,"%s\n",error_text);
+   }
-   exit(EXIT_FAILURE);
+   /* We add a separator at the end of dirc if not exists */
- }
+   l1 = strlen( dirc );                  /* length of directory */
- /*********************** vector *******************/
+   if( dirc[l1-1] != DIRSEPARATOR ){
- double *vector(int nl, int nh)
+     dirc[l1] =  DIRSEPARATOR;
- {
+     dirc[l1+1] = 0;
-   double *v;
+     printf(" DIRC3 = %s \n",dirc);
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   }
-   if (!v) nrerror("allocation failure in vector");
+   ss = strrchr( name, '.' );            /* find last / */
-   return v-nl+NR_END;
+   if (ss >0){
- }
+     ss++;
+     strcpy(ext,ss);                     /* save extension */
- /************************ free vector ******************/
+     l1= strlen( name);
- void free_vector(double*v, int nl, int nh)
+     l2= strlen(ss)+1;
- {
+     strncpy( finame, name, l1-l2);
-   free((FREE_ARG)(v+nl-NR_END));
+     finame[l1-l2]= 0;
- }
+   }
- /************************ivector *******************************/
+   return( 0 );                          /* we're done */
- int *ivector(long nl,long nh)
+ }
- {
-   int *v;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ /******************************************/
-   if (!v) nrerror("allocation failure in ivector");
-   return v-nl+NR_END;
+ void replace_back_to_slash(char *s, char*t)
- }
+ {
+   int i;
- /******************free ivector **************************/
+   int lg=0;
- void free_ivector(int *v, long nl, long nh)
+   i=0;
- {
+   lg=strlen(t);
-   free((FREE_ARG)(v+nl-NR_END));
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- /************************lvector *******************************/
+   }
- long *lvector(long nl,long nh)
+ }
- {
-   long *v;
+ char *trimbb(char *out, char *in)
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   if (!v) nrerror("allocation failure in ivector");
+   char *s;
-   return v-nl+NR_END;
+   s=out;
- }
+   while (*in != '\0'){
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- /******************free lvector **************************/
+       in++;
- void free_lvector(long *v, long nl, long nh)
+     }
- {
+     *out++ = *in++;
-   free((FREE_ARG)(v+nl-NR_END));
+   }
- }
+   *out='\0';
+   return s;
- /******************* imatrix *******************************/
+ }
- int **imatrix(long nrl, long nrh, long ncl, long nch)
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
  {
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
-   int **m;
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
-   /* allocate pointers to rows */
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   char *s, *t;
-   m += NR_END;
+   t=in;s=in;
-   m -= nrl;
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
+   }
-   /* allocate rows and set pointers to them */
+   if( *in == occ){
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+     *(alocc)='\0';
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     s=++in;
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   if (s == t) {/* occ not found */
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+     *(alocc-(in-s))='\0';
+     in=s;
-   /* return pointer to array of pointers to rows */
+   }
-   return m;
+   while ( *in != '\0'){
- }
+     *blocc++ = *in++;
+   }
- /****************** free_imatrix *************************/
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   *blocc='\0';
-       int **m;
+   return t;
-       long nch,ncl,nrh,nrl;
+ }
-      /* free an int matrix allocated by imatrix() */
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
  {
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-   free((FREE_ARG) (m+nrl-NR_END));
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- }
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
- /******************* matrix *******************************/
+   */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   char *s, *t;
- {
+   t=in;s=in;
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   while (*in != '\0'){
-   double **m;
+     while( *in == occ){
+       *blocc++ = *in++;
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+       s=in;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     }
-   m += NR_END;
+     *blocc++ = *in++;
-   m -= nrl;
+   }
+   if (s == t) /* occ not found */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     *(blocc-(in-s))='\0';
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   else
-   m[nrl] += NR_END;
+     *(blocc-(in-s)-1)='\0';
-   m[nrl] -= ncl;
+   in=s;
+   while ( *in != '\0'){
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+     *alocc++ = *in++;
-   return m;
+   }
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
-    */
+   *alocc='\0';
- }
+   return s;
+ }
- /*************************free matrix ************************/
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ int nbocc(char *s, char occ)
  {
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   int i,j=0;
-   free((FREE_ARG)(m+nrl-NR_END));
+   int lg=20;
- }
+   i=0;
+   lg=strlen(s);
- /******************* ma3x *******************************/
+   for(i=0; i<= lg; i++) {
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   if  (s[i] == occ ) j++;
- {
+   }
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   return j;
-   double ***m;
+ }
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /* { */
-   m += NR_END;
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   m -= nrl;
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   int i,lg,j,p=0; */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   i=0; */
-   m[nrl] += NR_END;
+ /*   lg=strlen(t); */
-   m[nrl] -= ncl;
+ /*   for(j=0; j<=lg-1; j++) { */
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*   } */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ /*   for(j=0; j<p; j++) { */
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ /*     (u[j] = t[j]); */
-   m[nrl][ncl] += NR_END;
+ /*   } */
-   m[nrl][ncl] -= nll;
+ /*      u[p]='\0'; */
-   for (j=ncl+1; j<=nch; j++)
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ /*    for(j=0; j<= lg; j++) { */
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   for (i=nrl+1; i<=nrh; i++) {
+ /*   } */
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ /* } */
-     for (j=ncl+1; j<=nch; j++)
-       m[i][j]=m[i][j-1]+nlay;
+ #ifdef _WIN32
-   }
+ char * strsep(char **pp, const char *delim)
-   return m;
+ {
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   char *p, *q;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   */
+   if ((p = *pp) == NULL)
- }
+     return 0;
+   if ((q = strpbrk (p, delim)) != NULL)
- /*************************free ma3x ************************/
+   {
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+     *pp = q + 1;
- {
+     *q = '\0';
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   }
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   else
-   free((FREE_ARG)(m+nrl-NR_END));
+     *pp = 0;
- }
+   return p;
+ }
- /*************** function subdirf ***********/
+ #endif
- char *subdirf(char fileres[])
- {
+ /********************** nrerror ********************/
-   /* Caution optionfilefiname is hidden */
-   strcpy(tmpout,optionfilefiname);
+ void nrerror(char error_text[])
-   strcat(tmpout,"/"); /* Add to the right */
+ {
-   strcat(tmpout,fileres);
+   fprintf(stderr,"ERREUR ...\n");
-   return tmpout;
+   fprintf(stderr,"%s\n",error_text);
- }
+   exit(EXIT_FAILURE);
+ }
- /*************** function subdirf2 ***********/
+ /*********************** vector *******************/
- char *subdirf2(char fileres[], char *preop)
+ double *vector(int nl, int nh)
  {
+   double *v;
-   /* Caution optionfilefiname is hidden */
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   strcpy(tmpout,optionfilefiname);
+   if (!v) nrerror("allocation failure in vector");
-   strcat(tmpout,"/");
+   return v-nl+NR_END;
-   strcat(tmpout,preop);
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /************************ free vector ******************/
- }
+ void free_vector(double*v, int nl, int nh)
+ {
- /*************** function subdirf3 ***********/
+   free((FREE_ARG)(v+nl-NR_END));
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ }
- {
+ /************************ivector *******************************/
-   /* Caution optionfilefiname is hidden */
+ int *ivector(long nl,long nh)
-   strcpy(tmpout,optionfilefiname);
+ {
-   strcat(tmpout,"/");
+   int *v;
-   strcat(tmpout,preop);
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   strcat(tmpout,preop2);
+   if (!v) nrerror("allocation failure in ivector");
-   strcat(tmpout,fileres);
+   return v-nl+NR_END;
-   return tmpout;
+ }
- }
+ /******************free ivector **************************/
- /***************** f1dim *************************/
+ void free_ivector(int *v, long nl, long nh)
- extern int ncom;
+ {
- extern double *pcom,*xicom;
+   free((FREE_ARG)(v+nl-NR_END));
- extern double (*nrfunc)(double []);
+ }
- double f1dim(double x)
+ /************************lvector *******************************/
- {
+ long *lvector(long nl,long nh)
-   int j;
+ {
-   double f;
+   long *v;
-   double *xt;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   if (!v) nrerror("allocation failure in ivector");
-   xt=vector(1,ncom);
+   return v-nl+NR_END;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ }
-   f=(*nrfunc)(xt);
-   free_vector(xt,1,ncom);
+ /******************free lvector **************************/
-   return f;
+ void free_lvector(long *v, long nl, long nh)
- }
+ {
+   free((FREE_ARG)(v+nl-NR_END));
- /*****************brent *************************/
+ }
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- {
+ /******************* imatrix *******************************/
-   int iter;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   double a,b,d,etemp;
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   double fu,fv,fw,fx;
+ {
-   double ftemp;
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   int **m;
-   double e=0.0;
+   /* allocate pointers to rows */
-   a=(ax < cx ? ax : cx);
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   b=(ax > cx ? ax : cx);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   x=w=v=bx;
+   m += NR_END;
-   fw=fv=fx=(*f)(x);
+   m -= nrl;
-   for (iter=1;iter<=ITMAX;iter++) {
-     xm=0.5*(a+b);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   /* allocate rows and set pointers to them */
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-     printf(".");fflush(stdout);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-     fprintf(ficlog,".");fflush(ficlog);
+   m[nrl] += NR_END;
- #ifdef DEBUG
+   m[nrl] -= ncl;
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- #endif
+   /* return pointer to array of pointers to rows */
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   return m;
-       *xmin=x;
+ }
-       return fx;
-     }
+ /****************** free_imatrix *************************/
-     ftemp=fu;
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-     if (fabs(e) > tol1) {
+       int **m;
-       r=(x-w)*(fx-fv);
+       long nch,ncl,nrh,nrl;
-       q=(x-v)*(fx-fw);
+      /* free an int matrix allocated by imatrix() */
-       p=(x-v)*q-(x-w)*r;
+ {
-       q=2.0*(q-r);
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-       if (q > 0.0) p = -p;
+   free((FREE_ARG) (m+nrl-NR_END));
-       q=fabs(q);
+ }
-       etemp=e;
-       e=d;
+ /******************* matrix *******************************/
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ {
-       else {
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-         d=p/q;
+   double **m;
-         u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-           d=SIGN(tol1,xm-x);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       }
+   m += NR_END;
-     } else {
+   m -= nrl;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-     fu=(*f)(u);
+   m[nrl] += NR_END;
-     if (fu <= fx) {
+   m[nrl] -= ncl;
-       if (u >= x) a=x; else b=x;
-       SHFT(v,w,x,u)
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-         SHFT(fv,fw,fx,fu)
+   return m;
-         } else {
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-           if (u < x) a=u; else b=u;
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-           if (fu <= fw || w == x) {
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-             v=w;
+    */
-             w=u;
+ }
-             fv=fw;
-             fw=fu;
+ /*************************free matrix ************************/
-           } else if (fu <= fv || v == x || v == w) {
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-             v=u;
+ {
-             fv=fu;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-           }
+   free((FREE_ARG)(m+nrl-NR_END));
-         }
+ }
-   }
-   nrerror("Too many iterations in brent");
+ /******************* ma3x *******************************/
-   *xmin=x;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-   return fx;
+ {
- }
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   double ***m;
- /****************** mnbrak ***********************/
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   if (!m) nrerror("allocation failure 1 in matrix()");
-             double (*func)(double))
+   m += NR_END;
- {
+   m -= nrl;
-   double ulim,u,r,q, dum;
-   double fu;
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   *fa=(*func)(*ax);
+   m[nrl] += NR_END;
-   *fb=(*func)(*bx);
+   m[nrl] -= ncl;
-   if (*fb > *fa) {
-     SHFT(dum,*ax,*bx,dum)
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-       SHFT(dum,*fb,*fa,dum)
-       }
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   *fc=(*func)(*cx);
+   m[nrl][ncl] += NR_END;
-   while (*fb > *fc) {
+   m[nrl][ncl] -= nll;
-     r=(*bx-*ax)*(*fb-*fc);
+   for (j=ncl+1; j<=nch; j++)
-     q=(*bx-*cx)*(*fb-*fa);
+     m[nrl][j]=m[nrl][j-1]+nlay;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   for (i=nrl+1; i<=nrh; i++) {
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-     if ((*bx-u)*(u-*cx) > 0.0) {
+     for (j=ncl+1; j<=nch; j++)
-       fu=(*func)(u);
+       m[i][j]=m[i][j-1]+nlay;
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+   }
-       fu=(*func)(u);
+   return m;
-       if (fu < *fc) {
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-           SHFT(*fb,*fc,fu,(*func)(u))
+   */
-           }
+ }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-       u=ulim;
+ /*************************free ma3x ************************/
-       fu=(*func)(u);
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-     } else {
+ {
-       u=(*cx)+GOLD*(*cx-*bx);
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-       fu=(*func)(u);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     }
+   free((FREE_ARG)(m+nrl-NR_END));
-     SHFT(*ax,*bx,*cx,u)
+ }
-       SHFT(*fa,*fb,*fc,fu)
-       }
+ /*************** function subdirf ***********/
- }
+ char *subdirf(char fileres[])
+ {
- /*************** linmin ************************/
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
- int ncom;
+   strcat(tmpout,"/"); /* Add to the right */
- double *pcom,*xicom;
+   strcat(tmpout,fileres);
- double (*nrfunc)(double []);
+   return tmpout;
+ }
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
- {
+ /*************** function subdirf2 ***********/
-   double brent(double ax, double bx, double cx,
+ char *subdirf2(char fileres[], char *preop)
-                double (*f)(double), double tol, double *xmin);
+ {
-   double f1dim(double x);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   /* Caution optionfilefiname is hidden */
-               double *fc, double (*func)(double));
+   strcpy(tmpout,optionfilefiname);
-   int j;
+   strcat(tmpout,"/");
-   double xx,xmin,bx,ax;
+   strcat(tmpout,preop);
-   double fx,fb,fa;
+   strcat(tmpout,fileres);
+   return tmpout;
-   ncom=n;
+ }
-   pcom=vector(1,n);
-   xicom=vector(1,n);
+ /*************** function subdirf3 ***********/
-   nrfunc=func;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   for (j=1;j<=n;j++) {
+ {
-     pcom[j]=p[j];
-     xicom[j]=xi[j];
+   /* Caution optionfilefiname is hidden */
-   }
+   strcpy(tmpout,optionfilefiname);
-   ax=0.0;
+   strcat(tmpout,"/");
-   xx=1.0;
+   strcat(tmpout,preop);
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   strcat(tmpout,preop2);
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   strcat(tmpout,fileres);
- #ifdef DEBUG
+   return tmpout;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ }
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- #endif
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   for (j=1;j<=n;j++) {
+ {
-     xi[j] *= xmin;
+   long sec_left, days, hours, minutes;
-     p[j] += xi[j];
+   days = (time_sec) / (60*60*24);
-   }
+   sec_left = (time_sec) % (60*60*24);
-   free_vector(xicom,1,n);
+   hours = (sec_left) / (60*60) ;
-   free_vector(pcom,1,n);
+   sec_left = (sec_left) %(60*60);
- }
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
- char *asc_diff_time(long time_sec, char ascdiff[])
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
- {
+   return ascdiff;
-   long sec_left, days, hours, minutes;
+ }
-   days = (time_sec) / (60*60*24);
-   sec_left = (time_sec) % (60*60*24);
+ /***************** f1dim *************************/
-   hours = (sec_left) / (60*60) ;
+ extern int ncom;
-   sec_left = (sec_left) %(60*60);
+ extern double *pcom,*xicom;
-   minutes = (sec_left) /60;
+ extern double (*nrfunc)(double []);
-   sec_left = (sec_left) % (60);
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ double f1dim(double x)
-   return ascdiff;
+ {
- }
+   int j;
+   double f;
- /*************** powell ************************/
+   double *xt;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-             double (*func)(double []))
+   xt=vector(1,ncom);
- {
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   void linmin(double p[], double xi[], int n, double *fret,
+   f=(*nrfunc)(xt);
-               double (*func)(double []));
+   free_vector(xt,1,ncom);
-   int i,ibig,j;
+   return f;
-   double del,t,*pt,*ptt,*xit;
+ }
-   double fp,fptt;
-   double *xits;
+ /*****************brent *************************/
-   int niterf, itmp;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+ {
-   pt=vector(1,n);
+   int iter;
-   ptt=vector(1,n);
+   double a,b,d,etemp;
-   xit=vector(1,n);
+   double fu=0,fv,fw,fx;
-   xits=vector(1,n);
+   double ftemp=0.;
-   *fret=(*func)(p);
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   double e=0.0;
-   for (*iter=1;;++(*iter)) {
-     fp=(*fret);
+   a=(ax < cx ? ax : cx);
-     ibig=0;
+   b=(ax > cx ? ax : cx);
-     del=0.0;
+   x=w=v=bx;
-     last_time=curr_time;
+   fw=fv=fx=(*f)(x);
-     (void) gettimeofday(&curr_time,&tzp);
+   for (iter=1;iter<=ITMAX;iter++) {
-     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);
+     xm=0.5*(a+b);
-     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);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-    for (i=1;i<=n;i++) {
+     printf(".");fflush(stdout);
-       printf(" %d %.12f",i, p[i]);
+     fprintf(ficlog,".");fflush(ficlog);
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+ #ifdef DEBUGBRENT
-       fprintf(ficrespow," %.12lf", p[i]);
+     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     }
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     printf("\n");
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-     fprintf(ficlog,"\n");
+ #endif
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-     if(*iter <=3){
+       *xmin=x;
-       tm = *localtime(&curr_time.tv_sec);
+       return fx;
-       strcpy(strcurr,asctime(&tm));
+     }
- /*       asctime_r(&tm,strcurr); */
+     ftemp=fu;
-       forecast_time=curr_time;
+     if (fabs(e) > tol1) {
-       itmp = strlen(strcurr);
+       r=(x-w)*(fx-fv);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+       q=(x-v)*(fx-fw);
-         strcurr[itmp-1]='\0';
+       p=(x-v)*q-(x-w)*r;
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       q=2.0*(q-r);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       if (q > 0.0) p = -p;
-       for(niterf=10;niterf<=30;niterf+=10){
+       q=fabs(q);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+       etemp=e;
-         tmf = *localtime(&forecast_time.tv_sec);
+       e=d;
- /*      asctime_r(&tmf,strfor); */
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         strcpy(strfor,asctime(&tmf));
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         itmp = strlen(strfor);
+       else {
-         if(strfor[itmp-1]=='\n')
+         d=p/q;
-         strfor[itmp-1]='\0';
+         u=x+d;
-         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);
+         if (u-a < tol2 || b-u < tol2)
-         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);
+           d=SIGN(tol1,xm-x);
        }
-     }
+     } else {
-     for (i=1;i<=n;i++) {
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+     }
-       fptt=(*fret);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
- #ifdef DEBUG
+     fu=(*f)(u);
-       printf("fret=%lf \n",*fret);
+     if (fu <= fx) {
-       fprintf(ficlog,"fret=%lf \n",*fret);
+       if (u >= x) a=x; else b=x;
- #endif
+       SHFT(v,w,x,u)
-       printf("%d",i);fflush(stdout);
+       SHFT(fv,fw,fx,fu)
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+     } else {
-       linmin(p,xit,n,fret,func);
+       if (u < x) a=u; else b=u;
-       if (fabs(fptt-(*fret)) > del) {
+       if (fu <= fw || w == x) {
-         del=fabs(fptt-(*fret));
+         v=w;
-         ibig=i;
+         w=u;
-       }
+         fv=fw;
- #ifdef DEBUG
+         fw=fu;
-       printf("%d %.12e",i,(*fret));
+       } else if (fu <= fv || v == x || v == w) {
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+         v=u;
-       for (j=1;j<=n;j++) {
+         fv=fu;
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+       }
-         printf(" x(%d)=%.12e",j,xit[j]);
+     }
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   }
-       }
+   nrerror("Too many iterations in brent");
-       for(j=1;j<=n;j++) {
+   *xmin=x;
-         printf(" p=%.12e",p[j]);
+   return fx;
-         fprintf(ficlog," p=%.12e",p[j]);
+ }
-       }
-       printf("\n");
+ /****************** mnbrak ***********************/
-       fprintf(ficlog,"\n");
- #endif
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-     }
+             double (*func)(double))
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
- #ifdef DEBUG
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
-       int k[2],l;
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
-       k[0]=1;
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
-       k[1]=-1;
+    */
-       printf("Max: %.12e",(*func)(p));
+   double ulim,u,r,q, dum;
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   double fu;
-       for (j=1;j<=n;j++) {
-         printf(" %.12e",p[j]);
+   *fa=(*func)(*ax);
-         fprintf(ficlog," %.12e",p[j]);
+   *fb=(*func)(*bx);
-       }
+   if (*fb > *fa) {
-       printf("\n");
+     SHFT(dum,*ax,*bx,dum)
-       fprintf(ficlog,"\n");
+     SHFT(dum,*fb,*fa,dum)
-       for(l=0;l<=1;l++) {
+   }
-         for (j=1;j<=n;j++) {
+   *cx=(*bx)+GOLD*(*bx-*ax);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+   *fc=(*func)(*cx);
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ #ifdef DEBUG
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-         }
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ #endif
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
-       }
+     r=(*bx-*ax)*(*fb-*fc);
- #endif
+     q=(*bx-*cx)*(*fb-*fa);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-       free_vector(xit,1,n);
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-       free_vector(xits,1,n);
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
-       free_vector(ptt,1,n);
+       fu=(*func)(u);
-       free_vector(pt,1,n);
+ #ifdef DEBUG
-       return;
+       /* f(x)=A(x-u)**2+f(u) */
-     }
+       double A, fparabu;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-     for (j=1;j<=n;j++) {
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-       ptt[j]=2.0*p[j]-pt[j];
+       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);
-       xit[j]=p[j]-pt[j];
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-       pt[j]=p[j];
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
-     }
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
-     fptt=(*func)(ptt);
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
-     if (fptt < fp) {
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ #endif
-       if (t < 0.0) {
+ #ifdef MNBRAKORIGINAL
-         linmin(p,xit,n,fret,func);
+ #else
-         for (j=1;j<=n;j++) {
+       if (fu > *fc) {
-           xi[j][ibig]=xi[j][n];
+ #ifdef DEBUG
-           xi[j][n]=xit[j];
+       printf("mnbrak4  fu > fc \n");
-         }
+       fprintf(ficlog, "mnbrak4 fu > fc\n");
- #ifdef DEBUG
+ #endif
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         /* 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 *\/  */
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
-         for(j=1;j<=n;j++){
+         dum=u; /* Shifting c and u */
-           printf(" %.12e",xit[j]);
+         u = *cx;
-           fprintf(ficlog," %.12e",xit[j]);
+         *cx = dum;
-         }
+         dum = fu;
-         printf("\n");
+         fu = *fc;
-         fprintf(ficlog,"\n");
+         *fc =dum;
- #endif
+       } else { /* end */
-       }
+ #ifdef DEBUG
-     }
+       printf("mnbrak3  fu < fc \n");
-   }
+       fprintf(ficlog, "mnbrak3 fu < fc\n");
- }
+ #endif
+         dum=u; /* Shifting c and u */
- /**** Prevalence limit (stable or period prevalence)  ****************/
+         u = *cx;
+         *cx = dum;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+         dum = fu;
- {
+         fu = *fc;
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+         *fc =dum;
-      matrix by transitions matrix until convergence is reached */
+       }
+ #endif
-   int i, ii,j,k;
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-   double min, max, maxmin, maxmax,sumnew=0.;
+ #ifdef DEBUG
-   double **matprod2();
+       printf("mnbrak2  u after c but before ulim\n");
-   double **out, cov[NCOVMAX], **pmij();
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
-   double **newm;
+ #endif
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+       fu=(*func)(u);
+       if (fu < *fc) {
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+ #ifdef DEBUG
-     for (j=1;j<=nlstate+ndeath;j++){
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
-     }
+ #endif
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-    cov[1]=1.;
+         SHFT(*fb,*fc,fu,(*func)(u))
+       }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ #ifdef DEBUG
-     newm=savm;
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
-     /* Covariates have to be included here again */
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
-      cov[2]=agefin;
+ #endif
+       u=ulim;
-       for (k=1; k<=cptcovn;k++) {
+       fu=(*func)(u);
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
-         /*      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]]);*/
+ #ifdef DEBUG
-       }
+       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
-       for (k=1; k<=cptcovprod;k++)
+ #endif
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       u=(*cx)+GOLD*(*cx-*bx);
+       fu=(*func)(u);
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     } /* end tests */
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     SHFT(*ax,*bx,*cx,u)
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     SHFT(*fa,*fb,*fc,fu)
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+ #ifdef DEBUG
+       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);
-     savm=oldm;
+       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);
-     oldm=newm;
+ #endif
-     maxmax=0.;
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
-     for(j=1;j<=nlstate;j++){
+ }
-       min=1.;
-       max=0.;
+ /*************** linmin ************************/
-       for(i=1; i<=nlstate; i++) {
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-         sumnew=0;
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+ the value of func at the returned location p . This is actually all accomplished by calling the
-         max=FMAX(max,prlim[i][j]);
+ routines mnbrak and brent .*/
-         min=FMIN(min,prlim[i][j]);
+ int ncom;
-       }
+ double *pcom,*xicom;
-       maxmin=max-min;
+ double (*nrfunc)(double []);
-       maxmax=FMAX(maxmax,maxmin);
-     }
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-     if(maxmax < ftolpl){
+ {
-       return prlim;
+   double brent(double ax, double bx, double cx,
-     }
+                double (*f)(double), double tol, double *xmin);
-   }
+   double f1dim(double x);
- }
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+               double *fc, double (*func)(double));
- /*************** transition probabilities ***************/
+   int j;
+   double xx,xmin,bx,ax;
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+   double fx,fb,fa;
- {
-   double s1, s2;
+   ncom=n;
-   /*double t34;*/
+   pcom=vector(1,n);
-   int i,j,j1, nc, ii, jj;
+   xicom=vector(1,n);
+   nrfunc=func;
-     for(i=1; i<= nlstate; i++){
+   for (j=1;j<=n;j++) {
-       for(j=1; j<i;j++){
+     pcom[j]=p[j];
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     xicom[j]=xi[j];
-           /*s2 += param[i][j][nc]*cov[nc];*/
+   }
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+   ax=0.0;
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+   xx=1.0;
-         }
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
-         ps[i][j]=s2;
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+ #ifdef DEBUG
-       }
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ #endif
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+   for (j=1;j<=n;j++) {
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+     xi[j] *= xmin;
-         }
+     p[j] += xi[j];
-         ps[i][j]=s2;
+   }
-       }
+   free_vector(xicom,1,n);
-     }
+   free_vector(pcom,1,n);
-     /*ps[3][2]=1;*/
+ }
-     for(i=1; i<= nlstate; i++){
-       s1=0;
+ /*************** powell ************************/
-       for(j=1; j<i; j++)
+ /*
-         s1+=exp(ps[i][j]);
+ Minimization of a function func of n variables. Input consists of an initial starting point
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-         s1+=exp(ps[i][j]);
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-       ps[i][i]=1./(s1+1.);
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-       for(j=1; j<i; j++)
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-       for(j=i+1; j<=nlstate+ndeath; j++)
+  */
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+             double (*func)(double []))
-     } /* end i */
+ {
+   void linmin(double p[], double xi[], int n, double *fret,
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+               double (*func)(double []));
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+   int i,ibig,j;
-         ps[ii][jj]=0;
+   double del,t,*pt,*ptt,*xit;
-         ps[ii][ii]=1;
+   double directest;
-       }
+   double fp,fptt;
-     }
+   double *xits;
+   int niterf, itmp;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   pt=vector(1,n);
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   ptt=vector(1,n);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+   xit=vector(1,n);
- /*       } */
+   xits=vector(1,n);
- /*       printf("\n "); */
+   *fret=(*func)(p);
- /*        } */
+   for (j=1;j<=n;j++) pt[j]=p[j];
- /*        printf("\n ");printf("%lf ",cov[2]); */
+     rcurr_time = time(NULL);
-        /*
+   for (*iter=1;;++(*iter)) {
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     fp=(*fret);
-       goto end;*/
+     ibig=0;
-     return ps;
+     del=0.0;
- }
+     rlast_time=rcurr_time;
+     /* (void) gettimeofday(&curr_time,&tzp); */
- /**************** Product of 2 matrices ******************/
+     rcurr_time = time(NULL);
+     curr_time = *localtime(&rcurr_time);
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
- {
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+    for (i=1;i<=n;i++) {
-   /* in, b, out are matrice of pointers which should have been initialized
+       printf(" %d %.12f",i, p[i]);
-      before: only the contents of out is modified. The function returns
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-      a pointer to pointers identical to out */
+       fprintf(ficrespow," %.12lf", p[i]);
-   long i, j, k;
+     }
-   for(i=nrl; i<= nrh; i++)
+     printf("\n");
-     for(k=ncolol; k<=ncoloh; k++)
+     fprintf(ficlog,"\n");
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-         out[i][k] +=in[i][j]*b[j][k];
+     if(*iter <=3){
+       tml = *localtime(&rcurr_time);
-   return out;
+       strcpy(strcurr,asctime(&tml));
- }
+       rforecast_time=rcurr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
- /************* Higher Matrix Product ***************/
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       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){
-   /* Computes the transition matrix starting at age 'age' over
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-      'nhstepm*hstepm*stepm' months (i.e. until
+         forecast_time = *localtime(&rforecast_time);
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+         strcpy(strfor,asctime(&forecast_time));
-      nhstepm*hstepm matrices.
+         itmp = strlen(strfor);
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+         if(strfor[itmp-1]=='\n')
-      (typically every 2 years instead of every month which is too big
+         strfor[itmp-1]='\0';
-      for the memory).
+         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);
-      Model is determined by parameters x and covariates have to be
+         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);
-      included manually here.
+       }
+     }
-      */
+     for (i=1;i<=n;i++) {
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-   int i, j, d, h, k;
+       fptt=(*fret);
-   double **out, cov[NCOVMAX];
+ #ifdef DEBUG
-   double **newm;
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-   /* Hstepm could be zero and should return the unit matrix */
+ #endif
-   for (i=1;i<=nlstate+ndeath;i++)
+       printf("%d",i);fflush(stdout);
-     for (j=1;j<=nlstate+ndeath;j++){
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
-     }
+                                        because that direction will be replaced unless the gain del is small
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+                                       in comparison with the 'probable' gain, mu^2, with the last average direction.
-   for(h=1; h <=nhstepm; h++){
+                                       Unless the n directions are conjugate some gain in the determinant may be obtained
-     for(d=1; d <=hstepm; d++){
+                                       with the new direction.
-       newm=savm;
+                                       */
-       /* Covariates have to be included here again */
+         del=fabs(fptt-(*fret));
-       cov[1]=1.;
+         ibig=i;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ #ifdef DEBUG
-       for (k=1; k<=cptcovage;k++)
+       printf("%d %.12e",i,(*fret));
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       for (k=1; k<=cptcovprod;k++)
+       for (j=1;j<=n;j++) {
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+         printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       }
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       for(j=1;j<=n;j++) {
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+         printf(" p(%d)=%.12e",j,p[j]);
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-       savm=oldm;
+       }
-       oldm=newm;
+       printf("\n");
-     }
+       fprintf(ficlog,"\n");
-     for(i=1; i<=nlstate+ndeath; i++)
+ #endif
-       for(j=1;j<=nlstate+ndeath;j++) {
+     } /* end i */
-         po[i][j][h]=newm[i][j];
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+ #ifdef DEBUG
-          */
+       int k[2],l;
-       }
+       k[0]=1;
-   } /* end h */
+       k[1]=-1;
-   return po;
+       printf("Max: %.12e",(*func)(p));
- }
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
+         printf(" %.12e",p[j]);
- /*************** log-likelihood *************/
+         fprintf(ficlog," %.12e",p[j]);
- double func( double *x)
+       }
- {
+       printf("\n");
-   int i, ii, j, k, mi, d, kk;
+       fprintf(ficlog,"\n");
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+       for(l=0;l<=1;l++) {
-   double **out;
+         for (j=1;j<=n;j++) {
-   double sw; /* Sum of weights */
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-   double lli; /* Individual log likelihood */
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   int s1, s2;
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   double bbh, survp;
+         }
-   long ipmx;
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   /*extern weight */
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   /* We are differentiating ll according to initial status */
+       }
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ #endif
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
-   */
+       free_vector(xit,1,n);
-   cov[1]=1.;
+       free_vector(xits,1,n);
+       free_vector(ptt,1,n);
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+       free_vector(pt,1,n);
+       return;
-   if(mle==1){
+     }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       ptt[j]=2.0*p[j]-pt[j];
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       xit[j]=p[j]-pt[j];
-           for (j=1;j<=nlstate+ndeath;j++){
+       pt[j]=p[j];
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     fptt=(*func)(ptt); /* f_3 */
-           }
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-         for(d=0; d<dh[mi][i]; d++){
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-           newm=savm;
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-           for (kk=1; kk<=cptcovage;kk++) {
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-           }
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef NRCORIGINAL
-           savm=oldm;
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
-           oldm=newm;
+ #else
-         } /* end mult */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
+       t= t- del*SQR(fp-fptt);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+ #endif
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+ #ifdef DEBUG
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       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);
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+       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);
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-          * probability in order to take into account the bias as a fraction of the way
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-          * -stepm/2 to stepm/2 .
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       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 stepm > 1 the results are less biased than in previous versions.
+ #endif
-          */
+ #ifdef POWELLORIGINAL
-         s1=s[mw[mi][i]][i];
+       if (t < 0.0) { /* Then we use it for new direction */
-         s2=s[mw[mi+1][i]][i];
+ #else
-         bbh=(double)bh[mi][i]/(double)stepm;
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-         /* bias bh is positive if real duration
+       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
-          * is higher than the multiple of stepm and negative otherwise.
+       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-          */
+       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-         if( s2 > nlstate){
+     }
-           /* i.e. if s2 is a death state and if the date of death is known
+       if (directest < 0.0) { /* Then we use it for new direction */
-              then the contribution to the likelihood is the probability to
+ #endif
-              die between last step unit time and current  step unit time,
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
-              which is also equal to probability to die before dh
+         for (j=1;j<=n;j++) {
-              minus probability to die before dh-stepm .
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-              In version up to 0.92 likelihood was computed
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-         as if date of death was unknown. Death was treated as any other
+         }
-         health state: the date of the interview describes the actual state
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-         and not the date of a change in health state. The former idea was
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-         to consider that at each interview the state was recorded
-         (healthy, disable or death) and IMaCh was corrected; but when we
+ #ifdef DEBUG
-         introduced the exact date of death then we should have modified
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         the contribution of an exact death to the likelihood. This new
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         contribution is smaller and very dependent of the step unit
+         for(j=1;j<=n;j++){
-         stepm. It is no more the probability to die between last interview
+           printf(" %.12e",xit[j]);
-         and month of death but the probability to survive from last
+           fprintf(ficlog," %.12e",xit[j]);
-         interview up to one month before death multiplied by the
+         }
-         probability to die within a month. Thanks to Chris
+         printf("\n");
-         Jackson for correcting this bug.  Former versions increased
+         fprintf(ficlog,"\n");
-         mortality artificially. The bad side is that we add another loop
+ #endif
-         which slows down the processing. The difference can be up to 10%
+       } /* end of t negative */
-         lower mortality.
+     } /* end if (fptt < fp)  */
-           */
+   }
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ }
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-         } else if  (s2==-2) {
-           for (j=1,survp=0. ; j<=nlstate; j++)
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ {
-           /*survp += out[s1][j]; */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-           lli= log(survp);
+      matrix by transitions matrix until convergence is reached */
-         }
+   int i, ii,j,k;
-         else if  (s2==-4) {
+   double min, max, maxmin, maxmax,sumnew=0.;
-           for (j=3,survp=0. ; j<=nlstate; j++)
+   /* double **matprod2(); */ /* test */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   double **out, cov[NCOVMAX+1], **pmij();
-           lli= log(survp);
+   double **newm;
-         }
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-         else if  (s2==-5) {
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1,survp=0. ; j<=2; j++)
+     for (j=1;j<=nlstate+ndeath;j++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           lli= log(survp);
+     }
-         }
+   cov[1]=1.;
-         else{
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+   /* Even if hstepm = 1, at least one multiplication by the unit 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 */
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-         }
+     newm=savm;
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+     /* Covariates have to be included here again */
-         /*if(lli ==000.0)*/
+     cov[2]=agefin;
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-         ipmx +=1;
+     for (k=1; k<=cptcovn;k++) {
-         sw += weight[i];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-       } /* end of wave */
+     }
-     } /* end of individual */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   }  else if(mle==2){
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-           for (j=1;j<=nlstate+ndeath;j++){
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-           }
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-         for(d=0; d<=dh[mi][i]; d++){
-           newm=savm;
+     savm=oldm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     oldm=newm;
-           for (kk=1; kk<=cptcovage;kk++) {
+     maxmax=0.;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     for(j=1;j<=nlstate;j++){
-           }
+       min=1.;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       max=0.;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for(i=1; i<=nlstate; i++) {
-           savm=oldm;
+         sumnew=0;
-           oldm=newm;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         } /* end mult */
+         prlim[i][j]= newm[i][j]/(1-sumnew);
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-         s1=s[mw[mi][i]][i];
+         max=FMAX(max,prlim[i][j]);
-         s2=s[mw[mi+1][i]][i];
+         min=FMIN(min,prlim[i][j]);
-         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 */
+       maxmin=max-min;
-         ipmx +=1;
+       maxmax=FMAX(maxmax,maxmin);
-         sw += weight[i];
+     } /* j loop */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     if(maxmax < ftolpl){
-       } /* end of wave */
+       return prlim;
-     } /* end of individual */
+     }
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+   } /* age loop */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   return prlim; /* should not reach here */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ }
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ /*************** transition probabilities ***************/
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ {
-           }
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-         for(d=0; d<dh[mi][i]; d++){
+      computes the probability to be observed in state j being in state i by appying the
-           newm=savm;
+      model to the ncovmodel covariates (including constant and age).
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-           for (kk=1; kk<=cptcovage;kk++) {
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      ncth covariate in the global vector x is given by the formula:
-           }
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-           savm=oldm;
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-           oldm=newm;
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-         } /* end mult */
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
-         s1=s[mw[mi][i]][i];
+   double s1, lnpijopii;
-         s2=s[mw[mi+1][i]][i];
+   /*double t34;*/
-         bbh=(double)bh[mi][i]/(double)stepm;
+   int i,j, nc, ii, jj;
-         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 */
-         ipmx +=1;
+     for(i=1; i<= nlstate; i++){
-         sw += weight[i];
+       for(j=1; j<i;j++){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-       } /* end of wave */
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-     } /* end of individual */
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       for(mi=1; mi<= wav[i]-1; mi++){
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       }
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-           }
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         for(d=0; d<dh[mi][i]; d++){
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-           newm=savm;
+         }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-           for (kk=1; kk<=cptcovage;kk++) {
+       }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     }
-           }
+     for(i=1; i<= nlstate; i++){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       s1=0;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for(j=1; j<i; j++){
-           savm=oldm;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           oldm=newm;
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         } /* end mult */
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
-         s1=s[mw[mi][i]][i];
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         s2=s[mw[mi+1][i]][i];
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         if( s2 > nlstate){
+       }
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         }else{
+       ps[i][i]=1./(s1+1.);
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       /* Computing other pijs */
-         }
+       for(j=1; j<i; j++)
-         ipmx +=1;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         sw += weight[i];
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-       } /* end of wave */
+     } /* end i */
-     } /* end of individual */
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         ps[ii][jj]=0;
-       for(mi=1; mi<= wav[i]-1; mi++){
+         ps[ii][ii]=1;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       }
-           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);
-           }
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         for(d=0; d<dh[mi][i]; d++){
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-           newm=savm;
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /*   } */
-           for (kk=1; kk<=cptcovage;kk++) {
+     /*   printf("\n "); */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     /* } */
-           }
+     /* printf("\n ");printf("%lf ",cov[2]);*/
+     /*
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       goto end;*/
-           savm=oldm;
+     return ps;
-           oldm=newm;
+ }
-         } /* end mult */
+ /**************** Product of 2 matrices ******************/
-         s1=s[mw[mi][i]][i];
-         s2=s[mw[mi+1][i]][i];
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ {
-         ipmx +=1;
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-         sw += weight[i];
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /* in, b, out are matrice of pointers which should have been initialized
-         /*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]);*/
+      before: only the contents of out is modified. The function returns
-       } /* end of wave */
+      a pointer to pointers identical to out */
-     } /* end of individual */
+   int i, j, k;
-   } /* End of if */
+   for(i=nrl; i<= nrh; i++)
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+     for(k=ncolol; k<=ncoloh; k++){
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+       out[i][k]=0.;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+       for(j=ncl; j<=nch; j++)
-   return -l;
+         out[i][k] +=in[i][j]*b[j][k];
- }
+     }
+   return out;
- /*************** log-likelihood *************/
+ }
- double funcone( double *x)
- {
-   /* Same as likeli but slower because of a lot of printf and if */
+ /************* Higher Matrix Product ***************/
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-   double **out;
+ {
-   double lli; /* Individual log likelihood */
+   /* Computes the transition matrix starting at age 'age' over
-   double llt;
+      'nhstepm*hstepm*stepm' months (i.e. until
-   int s1, s2;
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   double bbh, survp;
+      nhstepm*hstepm matrices.
-   /*extern weight */
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   /* We are differentiating ll according to initial status */
+      (typically every 2 years instead of every month which is too big
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+      for the memory).
-   /*for(i=1;i<imx;i++)
+      Model is determined by parameters x and covariates have to be
-     printf(" %d\n",s[4][i]);
+      included manually here.
-   */
-   cov[1]=1.;
+      */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   double **newm;
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     for(mi=1; mi<= wav[i]-1; mi++){
+   /* Hstepm could be zero and should return the unit matrix */
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+   for (i=1;i<=nlstate+ndeath;i++)
-         for (j=1;j<=nlstate+ndeath;j++){
+     for (j=1;j<=nlstate+ndeath;j++){
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         }
+     }
-       for(d=0; d<dh[mi][i]; d++){
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         newm=savm;
+   for(h=1; h <=nhstepm; h++){
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     for(d=1; d <=hstepm; d++){
-         for (kk=1; kk<=cptcovage;kk++) {
+       newm=savm;
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       /* Covariates have to be included here again */
-         }
+       cov[1]=1.;
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for (k=1; k<=cptcovn;k++)
-         savm=oldm;
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         oldm=newm;
+       for (k=1; k<=cptcovage;k++)
-       } /* end mult */
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-       s1=s[mw[mi][i]][i];
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       s2=s[mw[mi+1][i]][i];
-       bbh=(double)bh[mi][i]/(double)stepm;
-       /* bias is positive if real duration
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-        * is higher than the multiple of stepm and negative otherwise.
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-        */
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-         lli=log(out[s1][s2] - savm[s1][s2]);
+       savm=oldm;
-       } else if  (s2==-2) {
+       oldm=newm;
-         for (j=1,survp=0. ; j<=nlstate; j++)
+     }
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     for(i=1; i<=nlstate+ndeath; i++)
-         lli= log(survp);
+       for(j=1;j<=nlstate+ndeath;j++) {
-       }else if (mle==1){
+         po[i][j][h]=newm[i][j];
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-       } else if(mle==2){
+       }
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+     /*printf("h=%d ",h);*/
-       } else if(mle==3){  /* exponential inter-extrapolation */
+   } /* end h */
-         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+ /*     printf("\n H=%d \n",h); */
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+   return po;
-         lli=log(out[s1][s2]); /* Original formula */
+ }
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
-         lli=log(out[s1][s2]); /* Original formula */
+ #ifdef NLOPT
-       } /* End of if */
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-       ipmx +=1;
+   double fret;
-       sw += weight[i];
+   double *xt;
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   int 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]); */
+   myfunc_data *d2 = (myfunc_data *) pd;
-       if(globpr){
+ /* xt = (p1-1); */
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+   xt=vector(1,n);
-  %11.6f %11.6f %11.6f ", \
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-                 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]);
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-           llt +=ll[k]*gipmx/gsw;
+   printf("Function = %.12lf ",fret);
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-         }
+   printf("\n");
-         fprintf(ficresilk," %10.6f\n", -llt);
+  free_vector(xt,1,n);
-       }
+   return fret;
-     } /* end of wave */
+ }
-   } /* end of individual */
+ #endif
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ /*************** log-likelihood *************/
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ double func( double *x)
-   if(globpr==0){ /* First time we count the contributions and weights */
+ {
-     gipmx=ipmx;
+   int i, ii, j, k, mi, d, kk;
-     gsw=sw;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   }
+   double **out;
-   return -l;
+   double sw; /* Sum of weights */
- }
+   double lli; /* Individual log likelihood */
+   int s1, s2;
+   double bbh, survp;
- /*************** function likelione ***********/
+   long ipmx;
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+   /*extern weight */
- {
+   /* We are differentiating ll according to initial status */
-   /* This routine should help understanding what is done with
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-      the selection of individuals/waves and
+   /*for(i=1;i<imx;i++)
-      to check the exact contribution to the likelihood.
+     printf(" %d\n",s[4][i]);
-      Plotting could be done.
+   */
-    */
-   int k;
+   ++countcallfunc;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+   cov[1]=1.;
-     strcpy(fileresilk,"ilk");
-     strcat(fileresilk,fileres);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-       printf("Problem with resultfile: %s\n", fileresilk);
+   if(mle==1){
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     }
+       /* Computes the values of the ncovmodel covariates of the model
-     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");
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+          to be observed in j being in i according to the model.
-     for(k=1; k<=nlstate; k++)
+        */
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         cov[2+k]=covar[Tvar[k]][i];
-   }
+       }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   *fretone=(*funcone)(p);
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-   if(*globpri !=0){
+          has been calculated etc */
-     fclose(ficresilk);
+       for(mi=1; mi<= wav[i]-1; mi++){
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     fflush(fichtm);
+           for (j=1;j<=nlstate+ndeath;j++){
-   }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   return;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
+           }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
- /*********** Maximum Likelihood Estimation ***************/
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
- {
+           }
-   int i,j, iter;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   double **xi;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   double fret;
+           savm=oldm;
-   double fretone; /* Only one call to likelihood */
+           oldm=newm;
-   /*  char filerespow[FILENAMELENGTH];*/
+         } /* end mult */
-   xi=matrix(1,npar,1,npar);
-   for (i=1;i<=npar;i++)
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-     for (j=1;j<=npar;j++)
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-   strcpy(filerespow,"pow");
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-   strcat(filerespow,fileres);
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-     printf("Problem with resultfile: %s\n", filerespow);
+          * probability in order to take into account the bias as a fraction of the way
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-   }
+          * -stepm/2 to stepm/2 .
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+          * For stepm=1 the results are the same as for previous versions of Imach.
-   for (i=1;i<=nlstate;i++)
+          * For stepm > 1 the results are less biased than in previous versions.
-     for(j=1;j<=nlstate+ndeath;j++)
+          */
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+         s1=s[mw[mi][i]][i];
-   fprintf(ficrespow,"\n");
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+         /* bias bh is positive if real duration
+          * is higher than the multiple of stepm and negative otherwise.
-   free_matrix(xi,1,npar,1,npar);
+          */
-   fclose(ficrespow);
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         if( s2 > nlstate){
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           /* i.e. if s2 is a death state and if the date of death is known
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+              then the contribution to the likelihood is the probability to
+              die between last step unit time and current  step unit time,
- }
+              which is also equal to probability to die before dh
+              minus probability to die before dh-stepm .
- /**** Computes Hessian and covariance matrix ***/
+              In version up to 0.92 likelihood was computed
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+         as if date of death was unknown. Death was treated as any other
- {
+         health state: the date of the interview describes the actual state
-   double  **a,**y,*x,pd;
+         and not the date of a change in health state. The former idea was
-   double **hess;
+         to consider that at each interview the state was recorded
-   int i, j,jk;
+         (healthy, disable or death) and IMaCh was corrected; but when we
-   int *indx;
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+         contribution is smaller and very dependent of the step unit
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+         stepm. It is no more the probability to die between last interview
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+         and month of death but the probability to survive from last
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+         interview up to one month before death multiplied by the
-   double gompertz(double p[]);
+         probability to die within a month. Thanks to Chris
-   hess=matrix(1,npar,1,npar);
+         Jackson for correcting this bug.  Former versions increased
+         mortality artificially. The bad side is that we add another loop
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+         which slows down the processing. The difference can be up to 10%
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+         lower mortality.
-   for (i=1;i<=npar;i++){
+           */
-     printf("%d",i);fflush(stdout);
+         /* If, at the beginning of the maximization mostly, the
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+            cumulative probability or probability to be dead is
+            constant (ie = 1) over time d, the difference is equal to
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+.  out[s1][3] = savm[s1][3]: probability, being at state
+            s1 at precedent wave, to be dead a month before current
-     /*  printf(" %f ",p[i]);
+            wave is equal to probability, being at state s1 at
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+            precedent wave, to be dead at mont of the current
-   }
+            wave. Then the observed probability (that this person died)
+            is null according to current estimated parameter. In fact,
-   for (i=1;i<=npar;i++) {
+            it should be very low but not zero otherwise the log go to
-     for (j=1;j<=npar;j++)  {
+            infinity.
-       if (j>i) {
+         */
-         printf(".%d%d",i,j);fflush(stdout);
+ /* #ifdef INFINITYORIGINAL */
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+ /* #else */
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
-         hess[j][i]=hess[i][j];
+ /*          lli=log(mytinydouble); */
-         /*printf(" %lf ",hess[i][j]);*/
+ /*        else */
-       }
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
-     }
+ /* #endif */
-   }
+             lli=log(out[s1][s2] - savm[s1][s2]);
-   printf("\n");
-   fprintf(ficlog,"\n");
+         } else if  (s2==-2) {
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+           /*survp += out[s1][j]; */
+           lli= log(survp);
-   a=matrix(1,npar,1,npar);
+         }
-   y=matrix(1,npar,1,npar);
-   x=vector(1,npar);
+         else if  (s2==-4) {
-   indx=ivector(1,npar);
+           for (j=3,survp=0. ; j<=nlstate; j++)
-   for (i=1;i<=npar;i++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+           lli= log(survp);
-   ludcmp(a,npar,indx,&pd);
+         }
-   for (j=1;j<=npar;j++) {
+         else if  (s2==-5) {
-     for (i=1;i<=npar;i++) x[i]=0;
+           for (j=1,survp=0. ; j<=2; j++)
-     x[j]=1;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     lubksb(a,npar,indx,x);
+           lli= log(survp);
-     for (i=1;i<=npar;i++){
+         }
-       matcov[i][j]=x[i];
-     }
+         else{
-   }
+           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 */
-   printf("\n#Hessian matrix#\n");
+         }
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   for (i=1;i<=npar;i++) {
+         /*if(lli ==000.0)*/
-     for (j=1;j<=npar;j++) {
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-       printf("%.3e ",hess[i][j]);
+         ipmx +=1;
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+         sw += weight[i];
-     }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     printf("\n");
+         /* if (lli < log(mytinydouble)){ */
-     fprintf(ficlog,"\n");
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
-   }
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
+         /* } */
-   /* Recompute Inverse */
+       } /* end of wave */
-   for (i=1;i<=npar;i++)
+     } /* end of individual */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   }  else if(mle==2){
-   ludcmp(a,npar,indx,&pd);
+     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#Hessian matrix recomputed#\n");
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   for (j=1;j<=npar;j++) {
+           for (j=1;j<=nlstate+ndeath;j++){
-     for (i=1;i<=npar;i++) x[i]=0;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     x[j]=1;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     lubksb(a,npar,indx,x);
+           }
-     for (i=1;i<=npar;i++){
+         for(d=0; d<=dh[mi][i]; d++){
-       y[i][j]=x[i];
+           newm=savm;
-       printf("%.3e ",y[i][j]);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficlog,"%.3e ",y[i][j]);
+           for (kk=1; kk<=cptcovage;kk++) {
-     }
+             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;
+           oldm=newm;
-   free_matrix(a,1,npar,1,npar);
+         } /* end mult */
-   free_matrix(y,1,npar,1,npar);
-   free_vector(x,1,npar);
+         s1=s[mw[mi][i]][i];
-   free_ivector(indx,1,npar);
+         s2=s[mw[mi+1][i]][i];
-   free_matrix(hess,1,npar,1,npar);
+         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 */
+         ipmx +=1;
- }
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- /*************** hessian matrix ****************/
+       } /* end of wave */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+     } /* end of individual */
- {
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-   int i;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   int l=1, lmax=20;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   double k1,k2;
+       for(mi=1; mi<= wav[i]-1; mi++){
-   double p2[NPARMAX+1];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   double res;
+           for (j=1;j<=nlstate+ndeath;j++){
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double fx;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int k=0,kmax=10;
+           }
-   double l1;
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   fx=func(x);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+           for (kk=1; kk<=cptcovage;kk++) {
-   for(l=0 ; l <=lmax; l++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     l1=pow(10,l);
+           }
-     delts=delt;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     for(k=1 ; k <kmax; k=k+1){
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       delt = delta*(l1*k);
+           savm=oldm;
-       p2[theta]=x[theta] +delt;
+           oldm=newm;
-       k1=func(p2)-fx;
+         } /* end mult */
-       p2[theta]=x[theta]-delt;
-       k2=func(p2)-fx;
+         s1=s[mw[mi][i]][i];
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         s2=s[mw[mi+1][i]][i];
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+         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 */
- #ifdef DEBUG
+         ipmx +=1;
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+         sw += weight[i];
-       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);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- #endif
+       } /* end of wave */
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+     } /* end of individual */
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-         k=kmax;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       }
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+       for(mi=1; mi<= wav[i]-1; mi++){
-         k=kmax; l=lmax*10.;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       }
+           for (j=1;j<=nlstate+ndeath;j++){
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         delts=delt;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       }
+           }
-     }
+         for(d=0; d<dh[mi][i]; d++){
-   }
+           newm=savm;
-   delti[theta]=delts;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   return res;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
+           }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   int i;
+           savm=oldm;
-   int l=1, l1, lmax=20;
+           oldm=newm;
-   double k1,k2,k3,k4,res,fx;
+         } /* end mult */
-   double p2[NPARMAX+1];
-   int k;
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   fx=func(x);
+         if( s2 > nlstate){
-   for (k=1; k<=2; k++) {
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+         }else{
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         }
-     k1=func(p2)-fx;
+         ipmx +=1;
+         sw += weight[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ /*      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]); */
-     k2=func(p2)-fx;
+       } /* end of wave */
+     } /* end of individual */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     k3=func(p2)-fx;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+           for (j=1;j<=nlstate+ndeath;j++){
-     k4=func(p2)-fx;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
- #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(d=0; d<dh[mi][i]; d++){
-     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);
+           newm=savm;
- #endif
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   }
+           for (kk=1; kk<=cptcovage;kk++) {
-   return res;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
+           }
- /************** Inverse of matrix **************/
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- void ludcmp(double **a, int n, int *indx, double *d)
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- {
+           savm=oldm;
-   int i,imax,j,k;
+           oldm=newm;
-   double big,dum,sum,temp;
+         } /* end mult */
-   double *vv;
+         s1=s[mw[mi][i]][i];
-   vv=vector(1,n);
+         s2=s[mw[mi+1][i]][i];
-   *d=1.0;
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   for (i=1;i<=n;i++) {
+         ipmx +=1;
-     big=0.0;
+         sw += weight[i];
-     for (j=1;j<=n;j++)
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+         /*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]);*/
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+       } /* end of wave */
-     vv[i]=1.0/big;
+     } /* end of individual */
-   }
+   } /* End of if */
-   for (j=1;j<=n;j++) {
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     for (i=1;i<j;i++) {
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       sum=a[i][j];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   return -l;
-       a[i][j]=sum;
+ }
-     }
-     big=0.0;
+ /*************** log-likelihood *************/
-     for (i=j;i<=n;i++) {
+ double funcone( double *x)
-       sum=a[i][j];
+ {
-       for (k=1;k<j;k++)
+   /* Same as likeli but slower because of a lot of printf and if */
-         sum -= a[i][k]*a[k][j];
+   int i, ii, j, k, mi, d, kk;
-       a[i][j]=sum;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   double **out;
-         big=dum;
+   double lli; /* Individual log likelihood */
-         imax=i;
+   double llt;
-       }
+   int s1, s2;
-     }
+   double bbh, survp;
-     if (j != imax) {
+   /*extern weight */
-       for (k=1;k<=n;k++) {
+   /* We are differentiating ll according to initial status */
-         dum=a[imax][k];
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         a[imax][k]=a[j][k];
+   /*for(i=1;i<imx;i++)
-         a[j][k]=dum;
+     printf(" %d\n",s[4][i]);
-       }
+   */
-       *d = -(*d);
+   cov[1]=1.;
-       vv[imax]=vv[j];
-     }
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     indx[j]=imax;
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     if (j != n) {
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       dum=1.0/(a[j][j]);
+     for(mi=1; mi<= wav[i]-1; mi++){
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-     }
+         for (j=1;j<=nlstate+ndeath;j++){
-   }
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   free_vector(vv,1,n);  /* Doesn't work */
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
- ;
+         }
- }
+       for(d=0; d<dh[mi][i]; d++){
+         newm=savm;
- void lubksb(double **a, int n, int *indx, double b[])
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- {
+         for (kk=1; kk<=cptcovage;kk++) {
-   int i,ii=0,ip,j;
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   double sum;
+         }
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   for (i=1;i<=n;i++) {
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     ip=indx[i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     sum=b[ip];
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-     b[ip]=b[i];
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-     if (ii)
+         savm=oldm;
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+         oldm=newm;
-     else if (sum) ii=i;
+       } /* end mult */
-     b[i]=sum;
-   }
+       s1=s[mw[mi][i]][i];
-   for (i=n;i>=1;i--) {
+       s2=s[mw[mi+1][i]][i];
-     sum=b[i];
+       bbh=(double)bh[mi][i]/(double)stepm;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+       /* bias is positive if real duration
-     b[i]=sum/a[i][i];
+        * is higher than the multiple of stepm and negative otherwise.
-   }
+        */
- }
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
- void pstamp(FILE *fichier)
+       } else if  (s2==-2) {
- {
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- }
+         lli= log(survp);
+       }else if (mle==1){
- /************ Frequencies ********************/
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- 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[])
+       } else if(mle==2){
- {  /* Some frequencies */
+         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, m, jk, k1,i1, j1, bool, z1,z2,j;
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   int first;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   double ***freq; /* Frequencies */
+         lli=log(out[s1][s2]); /* Original formula */
-   double *pp, **prop;
+       } else{  /* mle=0 back to 1 */
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   char fileresp[FILENAMELENGTH];
+         /*lli=log(out[s1][s2]); */ /* Original formula */
+       } /* End of if */
-   pp=vector(1,nlstate);
+       ipmx +=1;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       sw += weight[i];
-   strcpy(fileresp,"p");
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   strcat(fileresp,fileres);
+       /*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]); */
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+       if(globpr){
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+  %11.6f %11.6f %11.6f ", \
-     exit(0);
+                 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]);
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   j1=0;
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   j=cptcoveff;
+         }
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
-   first=1;
+     } /* end of wave */
+   } /* end of individual */
-   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 */
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   if(globpr==0){ /* First time we count the contributions and weights */
-         scanf("%d", i);*/
+     gipmx=ipmx;
-       for (i=-5; i<=nlstate+ndeath; i++)
+     gsw=sw;
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   }
-           for(m=iagemin; m <= iagemax+3; m++)
+   return -l;
-             freq[i][jk][m]=0;
+ }
-     for (i=1; i<=nlstate; i++)
-       for(m=iagemin; m <= iagemax+3; m++)
+ /*************** function likelione ***********/
-         prop[i][m]=0;
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
-       dateintsum=0;
+   /* This routine should help understanding what is done with
-       k2cpt=0;
+      the selection of individuals/waves and
-       for (i=1; i<=imx; i++) {
+      to check the exact contribution to the likelihood.
-         bool=1;
+      Plotting could be done.
-         if  (cptcovn>0) {
+    */
-           for (z1=1; z1<=cptcoveff; z1++)
+   int k;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-         }
+     strcpy(fileresilk,"ilk");
-         if (bool==1){
+     strcat(fileresilk,fileres);
-           for(m=firstpass; m<=lastpass; m++){
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-             k2=anint[m][i]+(mint[m][i]/12.);
+       printf("Problem with resultfile: %s\n", fileresilk);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     }
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-               if (m<lastpass) {
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     for(k=1; k<=nlstate; k++)
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-               }
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-                 dateintsum=dateintsum+k2;
+   *fretone=(*funcone)(p);
-                 k2cpt++;
+   if(*globpri !=0){
-               }
+     fclose(ficresilk);
-               /*}*/
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-           }
+     fflush(fichtm);
-         }
+   }
-       }
+   return;
+ }
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
-       if  (cptcovn>0) {
+ /*********** Maximum Likelihood Estimation ***************/
-         fprintf(ficresp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-         fprintf(ficresp, "**********\n#");
+ {
-       }
+   int i,j, iter=0;
-       for(i=1; i<=nlstate;i++)
+   double **xi;
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   double fret;
-       fprintf(ficresp, "\n");
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
-       for(i=iagemin; i <= iagemax+3; i++){
-         if(i==iagemax+3){
+ #ifdef NLOPT
-           fprintf(ficlog,"Total");
+   int creturn;
-         }else{
+   nlopt_opt opt;
-           if(first==1){
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-             first=0;
+   double *lb;
-             printf("See log file for details...\n");
+   double minf; /* the minimum objective value, upon return */
-           }
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-           fprintf(ficlog,"Age %d", i);
+   myfunc_data dinst, *d = &dinst;
-         }
+ #endif
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
+   xi=matrix(1,npar,1,npar);
-         }
+   for (i=1;i<=npar;i++)
-         for(jk=1; jk <=nlstate ; jk++){
+     for (j=1;j<=npar;j++)
-           for(m=-1, pos=0; m <=0 ; m++)
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-             pos += freq[jk][m][i];
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-           if(pp[jk]>=1.e-10){
+   strcpy(filerespow,"pow");
-             if(first==1){
+   strcat(filerespow,fileres);
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-             }
+     printf("Problem with resultfile: %s\n", filerespow);
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-           }else{
+   }
-             if(first==1)
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (i=1;i<=nlstate;i++)
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     for(j=1;j<=nlstate+ndeath;j++)
-           }
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-         }
+   fprintf(ficrespow,"\n");
+ #ifdef POWELL
-         for(jk=1; jk <=nlstate ; jk++){
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+ #endif
-             pp[jk] += freq[jk][m][i];
-         }
+ #ifdef NLOPT
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+ #ifdef NEWUOA
-           pos += pp[jk];
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-           posprop += prop[jk][i];
+ #else
-         }
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-         for(jk=1; jk <=nlstate ; jk++){
+ #endif
-           if(pos>=1.e-5){
+   lb=vector(0,npar-1);
-             if(first==1)
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   nlopt_set_lower_bounds(opt, lb);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   nlopt_set_initial_step1(opt, 0.1);
-           }else{
-             if(first==1)
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   d->function = func;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-           }
+   nlopt_set_min_objective(opt, myfunc, d);
-           if( i <= iagemax){
+   nlopt_set_xtol_rel(opt, ftol);
-             if(pos>=1.e-5){
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+     printf("nlopt failed! %d\n",creturn);
-               /*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]);*/
+   else {
-             }
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-             else
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+     iter=1; /* not equal */
-           }
+   }
-         }
+   nlopt_destroy(opt);
+ #endif
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+   free_matrix(xi,1,npar,1,npar);
-           for(m=-1; m <=nlstate+ndeath; m++)
+   fclose(ficrespow);
-             if(freq[jk][m][i] !=0 ) {
+   printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-             if(first==1)
+   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-             }
+ }
-         if(i <= iagemax)
-           fprintf(ficresp,"\n");
+ /**** Computes Hessian and covariance matrix ***/
-         if(first==1)
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-           printf("Others in log...\n");
+ {
-         fprintf(ficlog,"\n");
+   double  **a,**y,*x,pd;
-       }
+   double **hess;
-     }
+   int i, j;
-   }
+   int *indx;
-   dateintmean=dateintsum/k2cpt;
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   fclose(ficresp);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   free_vector(pp,1,nlstate);
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   double gompertz(double p[]);
-   /* End of Freq */
+   hess=matrix(1,npar,1,npar);
- }
+   printf("\nCalculation of the hessian matrix. Wait...\n");
- /************ Prevalence ********************/
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+   for (i=1;i<=npar;i++){
- {
+     printf("%d",i);fflush(stdout);
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
-      We still use firstpass and lastpass as another selection.
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-   */
+     /*  printf(" %f ",p[i]);
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-   double ***freq; /* Frequencies */
+   }
-   double *pp, **prop;
-   double pos,posprop;
+   for (i=1;i<=npar;i++) {
-   double  y2; /* in fractional years */
+     for (j=1;j<=npar;j++)  {
-   int iagemin, iagemax;
+       if (j>i) {
+         printf(".%d%d",i,j);fflush(stdout);
-   iagemin= (int) agemin;
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-   iagemax= (int) agemax;
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         hess[j][i]=hess[i][j];
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+         /*printf(" %lf ",hess[i][j]);*/
-   j1=0;
+       }
+     }
-   j=cptcoveff;
+   }
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   printf("\n");
+   fprintf(ficlog,"\n");
-   for(k1=1; k1<=j;k1++){
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-       j1++;
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       for (i=1; i<=nlstate; i++)
+   a=matrix(1,npar,1,npar);
-         for(m=iagemin; m <= iagemax+3; m++)
+   y=matrix(1,npar,1,npar);
-           prop[i][m]=0.0;
+   x=vector(1,npar);
+   indx=ivector(1,npar);
-       for (i=1; i<=imx; i++) { /* Each individual */
+   for (i=1;i<=npar;i++)
-         bool=1;
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-         if  (cptcovn>0) {
+   ludcmp(a,npar,indx,&pd);
-           for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   for (j=1;j<=npar;j++) {
-               bool=0;
+     for (i=1;i<=npar;i++) x[i]=0;
-         }
+     x[j]=1;
-         if (bool==1) {
+     lubksb(a,npar,indx,x);
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+     for (i=1;i<=npar;i++){
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+       matcov[i][j]=x[i];
-             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;
-               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);
+   printf("\n#Hessian matrix#\n");
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+   for (i=1;i<=npar;i++) {
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     for (j=1;j<=npar;j++) {
-                 prop[s[m][i]][iagemax+3] += weight[i];
+       printf("%.3e ",hess[i][j]);
-               }
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-             }
+     }
-           } /* end selection of waves */
+     printf("\n");
-         }
+     fprintf(ficlog,"\n");
-       }
+   }
-       for(i=iagemin; i <= iagemax+3; i++){
+   /* Recompute Inverse */
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+   for (i=1;i<=npar;i++)
-           posprop += prop[jk][i];
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-         }
+   ludcmp(a,npar,indx,&pd);
-         for(jk=1; jk <=nlstate ; jk++){
+   /*  printf("\n#Hessian matrix recomputed#\n");
-           if( i <=  iagemax){
-             if(posprop>=1.e-5){
+   for (j=1;j<=npar;j++) {
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+     for (i=1;i<=npar;i++) x[i]=0;
-             }
+     x[j]=1;
-           }
+     lubksb(a,npar,indx,x);
-         }/* end jk */
+     for (i=1;i<=npar;i++){
-       }/* end i */
+       y[i][j]=x[i];
-     } /* end i1 */
+       printf("%.3e ",y[i][j]);
-   } /* end k1 */
+       fprintf(ficlog,"%.3e ",y[i][j]);
+     }
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+     printf("\n");
-   /*free_vector(pp,1,nlstate);*/
+     fprintf(ficlog,"\n");
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   }
- }  /* End of prevalence */
+   */
- /************* Waves Concatenation ***************/
+   free_matrix(a,1,npar,1,npar);
+   free_matrix(y,1,npar,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_vector(x,1,npar);
- {
+   free_ivector(indx,1,npar);
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   free_matrix(hess,1,npar,1,npar);
-      Death is a valid wave (if date is known).
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+ }
-      and mw[mi+1][i]. dh depends on stepm.
-      */
+ /*************** hessian matrix ****************/
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-   int i, mi, m;
+ {
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   int i;
-      double sum=0., jmean=0.;*/
+   int l=1, lmax=20;
-   int first;
+   double k1,k2;
-   int j, k=0,jk, ju, jl;
+   double p2[MAXPARM+1]; /* identical to x */
-   double sum=0.;
+   double res;
-   first=0;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   jmin=1e+5;
+   double fx;
-   jmax=-1;
+   int k=0,kmax=10;
-   jmean=0.;
+   double l1;
-   for(i=1; i<=imx; i++){
-     mi=0;
+   fx=func(x);
-     m=firstpass;
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-     while(s[m][i] <= nlstate){
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+     l1=pow(10,l);
-         mw[++mi][i]=m;
+     delts=delt;
-       if(m >=lastpass)
+     for(k=1 ; k <kmax; k=k+1){
-         break;
+       delt = delta*(l1*k);
-       else
+       p2[theta]=x[theta] +delt;
-         m++;
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-     }/* end while */
+       p2[theta]=x[theta]-delt;
-     if (s[m][i] > nlstate){
+       k2=func(p2)-fx;
-       mi++;     /* Death is another wave */
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-       /* if(mi==0)  never been interviewed correctly before death */
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-          /* Only death is a correct wave */
-       mw[mi][i]=m;
+ #ifdef DEBUGHESS
-     }
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-     wav[i]=mi;
+ #endif
-     if(mi==0){
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-       nbwarn++;
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-       if(first==0){
+         k=kmax;
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+       }
-         first=1;
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-       }
+         k=kmax; l=lmax*10;
-       if(first==1){
+       }
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-       }
+         delts=delt;
-     } /* end mi==0 */
+       }
-   } /* End individuals */
+     }
+   }
-   for(i=1; i<=imx; i++){
+   delti[theta]=delts;
-     for(mi=1; mi<wav[i];mi++){
+   return res;
-       if (stepm <=0)
-         dh[mi][i]=1;
+ }
-       else{
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-           if (agedc[i] < 2*AGESUP) {
+ {
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+   int i;
-             if(j==0) j=1;  /* Survives at least one month after exam */
+   int l=1, lmax=20;
-             else if(j<0){
+   double k1,k2,k3,k4,res,fx;
-               nberr++;
+   double p2[MAXPARM+1];
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   int k;
-               j=1; /* Temporary Dangerous patch */
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   fx=func(x);
-               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 (k=1; k<=2; k++) {
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-             }
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-             k=k+1;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-             if (j >= jmax){
+     k1=func(p2)-fx;
-               jmax=j;
-               ijmax=i;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-             }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-             if (j <= jmin){
+     k2=func(p2)-fx;
-               jmin=j;
-               ijmin=i;
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-             }
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-             sum=sum+j;
+     k3=func(p2)-fx;
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-           }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-         }
+     k4=func(p2)-fx;
-         else{
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ #ifdef DEBUG
- /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+     printf("%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);
-           k=k+1;
+ #endif
-           if (j >= jmax) {
+   }
-             jmax=j;
+   return res;
-             ijmax=i;
+ }
-           }
-           else if (j <= jmin){
+ /************** Inverse of matrix **************/
-             jmin=j;
+ void ludcmp(double **a, int n, int *indx, double *d)
-             ijmin=i;
+ {
-           }
+   int i,imax,j,k;
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   double big,dum,sum,temp;
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+   double *vv;
-           if(j<0){
-             nberr++;
+   vv=vector(1,n);
-             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]);
+   *d=1.0;
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   for (i=1;i<=n;i++) {
-           }
+     big=0.0;
-           sum=sum+j;
+     for (j=1;j<=n;j++)
-         }
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-         jk= j/stepm;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-         jl= j -jk*stepm;
+     vv[i]=1.0/big;
-         ju= j -(jk+1)*stepm;
+   }
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   for (j=1;j<=n;j++) {
-           if(jl==0){
+     for (i=1;i<j;i++) {
-             dh[mi][i]=jk;
+       sum=a[i][j];
-             bh[mi][i]=0;
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-           }else{ /* We want a negative bias in order to only have interpolation ie
+       a[i][j]=sum;
-                   * at the price of an extra matrix product in likelihood */
+     }
-             dh[mi][i]=jk+1;
+     big=0.0;
-             bh[mi][i]=ju;
+     for (i=j;i<=n;i++) {
-           }
+       sum=a[i][j];
-         }else{
+       for (k=1;k<j;k++)
-           if(jl <= -ju){
+         sum -= a[i][k]*a[k][j];
-             dh[mi][i]=jk;
+       a[i][j]=sum;
-             bh[mi][i]=jl;       /* bias is positive if real duration
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-                                  * is higher than the multiple of stepm and negative otherwise.
+         big=dum;
-                                  */
+         imax=i;
-           }
+       }
-           else{
+     }
-             dh[mi][i]=jk+1;
+     if (j != imax) {
-             bh[mi][i]=ju;
+       for (k=1;k<=n;k++) {
-           }
+         dum=a[imax][k];
-           if(dh[mi][i]==0){
+         a[imax][k]=a[j][k];
-             dh[mi][i]=1; /* At least one step */
+         a[j][k]=dum;
-             bh[mi][i]=ju; /* At least one step */
+       }
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+       *d = -(*d);
-           }
+       vv[imax]=vv[j];
-         } /* end if mle */
+     }
-       }
+     indx[j]=imax;
-     } /* end wave */
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   }
+     if (j != n) {
-   jmean=sum/k;
+       dum=1.0/(a[j][j]);
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   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);
+     }
-  }
+   }
+   free_vector(vv,1,n);  /* Doesn't work */
- /*********** Tricode ****************************/
+ ;
- void tricode(int *Tvar, int **nbcode, int imx)
+ }
- {
+ void lubksb(double **a, int n, int *indx, double b[])
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+ {
-   int cptcode=0;
+   int i,ii=0,ip,j;
-   cptcoveff=0;
+   double sum;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (i=1;i<=n;i++) {
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+     ip=indx[i];
+     sum=b[ip];
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+     b[ip]=b[i];
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+     if (ii)
-                                modality*/
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+     else if (sum) ii=i;
-       Ndum[ij]++; /*store the modality */
+     b[i]=sum;
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+   }
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+   for (i=n;i>=1;i--) {
-                                        Tvar[j]. If V=sex and male is 0 and
+     sum=b[i];
-                                        female is 1, then  cptcode=1.*/
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-     }
+     b[i]=sum/a[i][i];
+   }
-     for (i=0; i<=cptcode; i++) {
+ }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
-     }
+ void pstamp(FILE *fichier)
+ {
-     ij=1;
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-     for (i=1; i<=ncodemax[j]; i++) {
+ }
-       for (k=0; k<= maxncov; k++) {
-         if (Ndum[k] != 0) {
+ /************ Frequencies ********************/
-           nbcode[Tvar[j]][ij]=k;
+ 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[])
-           /* 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; */
+ {  /* Some frequencies */
-           ij++;
+   int i, m, jk, j1, bool, z1,j;
-         }
+   int first;
-         if (ij > ncodemax[j]) break;
+   double ***freq; /* Frequencies */
-       }
+   double *pp, **prop;
-     }
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   }
+   char fileresp[FILENAMELENGTH];
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   pp=vector(1,nlstate);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-  for (i=1; i<=ncovmodel-2; i++) {
+   strcpy(fileresp,"p");
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+   strcat(fileresp,fileres);
-    ij=Tvar[i];
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-    Ndum[ij]++;
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-  }
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+     exit(0);
-  ij=1;
+   }
-  for (i=1; i<= maxncov; i++) {
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+   j1=0;
-      Tvaraff[ij]=i; /*For printing */
-      ij++;
+   j=cptcoveff;
-    }
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-  }
+   first=1;
-  cptcoveff=ij-1; /*Number of simple covariates*/
- }
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
- /*********** Health Expectancies ****************/
+   /*    j1++; */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
- 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[] )
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         scanf("%d", i);*/
- {
+       for (i=-5; i<=nlstate+ndeath; i++)
-   /* Health expectancies, no variances */
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+           for(m=iagemin; m <= iagemax+3; m++)
-   double age, agelim, hf;
+             freq[i][jk][m]=0;
-   double ***p3mat;
-   double eip;
+       for (i=1; i<=nlstate; i++)
+         for(m=iagemin; m <= iagemax+3; m++)
-   pstamp(ficreseij);
+           prop[i][m]=0;
-   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");
+       dateintsum=0;
-   for(i=1; i<=nlstate;i++){
+       k2cpt=0;
-     for(j=1; j<=nlstate;j++){
+       for (i=1; i<=imx; i++) {
-       fprintf(ficreseij," e%1d%1d ",i,j);
+         bool=1;
-     }
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-     fprintf(ficreseij," e%1d. ",i);
+           for (z1=1; z1<=cptcoveff; z1++)
-   }
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-   fprintf(ficreseij,"\n");
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               bool=0;
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-   if(estepm < stepm){
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-   }
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-   else  hstepm=estepm;
+             }
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+         }
-    * This is mainly to measure the difference between two models: for example
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+         if (bool==1){
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+           for(m=firstpass; m<=lastpass; m++){
-    * progression in between and thus overestimating or underestimating according
+             k2=anint[m][i]+(mint[m][i]/12.);
-    * to the curvature of the survival function. If, for the same date, we
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-    * to compare the new estimate of Life expectancy with the same linear
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-    * hypothesis. A more precise result, taking into account a more precise
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-    * curvature will be obtained if estepm is as small as stepm. */
+               if (m<lastpass) {
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-   /* For example we decided to compute the life expectancy with the smallest unit */
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+               }
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-      Look at hpijx to understand the reason of that which relies in memory size
+                 dateintsum=dateintsum+k2;
-      and note for a fixed period like estepm months */
+                 k2cpt++;
-   /* 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
+               /*}*/
-      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.
+       } /* end i */
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       pstamp(ficresp);
-   agelim=AGESUP;
+       if  (cptcovn>0) {
-   /* If stepm=6 months */
+         fprintf(ficresp, "\n#********** Variable ");
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         fprintf(ficresp, "**********\n#");
+         fprintf(ficlog, "\n#********** Variable ");
- /* nhstepm age range expressed in number of stepm */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   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;*/
+       for(i=1; i<=nlstate;i++)
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficresp, "\n");
-   for (age=bage; age<=fage; age ++){
+       for(i=iagemin; i <= iagemax+3; i++){
+         if(i==iagemax+3){
+           fprintf(ficlog,"Total");
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+         }else{
+           if(first==1){
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             first=0;
+             printf("See log file for details...\n");
-     printf("%d|",(int)age);fflush(stdout);
+           }
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           fprintf(ficlog,"Age %d", i);
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-     /* Computing expectancies */
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-     for(i=1; i<=nlstate;i++)
+             pp[jk] += freq[jk][m][i];
-       for(j=1; j<=nlstate;j++)
+         }
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+         for(jk=1; jk <=nlstate ; jk++){
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[jk][m][i];
-           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+           if(pp[jk]>=1.e-10){
+             if(first==1){
-         }
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+             }
-     fprintf(ficreseij,"%3.0f",age );
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-     for(i=1; i<=nlstate;i++){
+           }else{
-       eip=0;
+             if(first==1)
-       for(j=1; j<=nlstate;j++){
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         eip +=eij[i][j][(int)age];
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+           }
-       }
+         }
-       fprintf(ficreseij,"%9.4f", eip );
-     }
+         for(jk=1; jk <=nlstate ; jk++){
-     fprintf(ficreseij,"\n");
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+             pp[jk] += freq[jk][m][i];
-   }
+         }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-   printf("\n");
+           pos += pp[jk];
-   fprintf(ficlog,"\n");
+           posprop += prop[jk][i];
+         }
- }
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5){
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- {
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   /* Covariances of health expectancies eij and of total life expectancies according
+           }else{
-    to initial status i, ei. .
+             if(first==1)
-   */
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   double age, agelim, hf;
+           }
-   double ***p3matp, ***p3matm, ***varhe;
+           if( i <= iagemax){
-   double **dnewm,**doldm;
+             if(pos>=1.e-5){
-   double *xp, *xm;
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   double **gp, **gm;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   double ***gradg, ***trgradg;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   int theta;
+             }
+             else
-   double eip, vip;
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+           }
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+         }
-   xp=vector(1,npar);
-   xm=vector(1,npar);
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+           for(m=-1; m <=nlstate+ndeath; m++)
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+             if(freq[jk][m][i] !=0 ) {
+             if(first==1)
-   pstamp(ficresstdeij);
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   fprintf(ficresstdeij,"# Age");
+             }
-   for(i=1; i<=nlstate;i++){
+         if(i <= iagemax)
-     for(j=1; j<=nlstate;j++)
+           fprintf(ficresp,"\n");
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+         if(first==1)
-     fprintf(ficresstdeij," e%1d. ",i);
+           printf("Others in log...\n");
-   }
+         fprintf(ficlog,"\n");
-   fprintf(ficresstdeij,"\n");
+       }
+       /*}*/
-   pstamp(ficrescveij);
+   }
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   dateintmean=dateintsum/k2cpt;
-   fprintf(ficrescveij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   fclose(ficresp);
-     for(j=1; j<=nlstate;j++){
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-       cptj= (j-1)*nlstate+i;
+   free_vector(pp,1,nlstate);
-       for(i2=1; i2<=nlstate;i2++)
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-         for(j2=1; j2<=nlstate;j2++){
+   /* End of Freq */
-           cptj2= (j2-1)*nlstate+i2;
+ }
-           if(cptj2 <= cptj)
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+ /************ Prevalence ********************/
-         }
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
-     }
+ {
-   fprintf(ficrescveij,"\n");
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-   if(estepm < stepm){
+      We still use firstpass and lastpass as another selection.
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   */
-   }
-   else  hstepm=estepm;
+   int i, m, jk, j1, bool, z1,j;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
-    * This is mainly to measure the difference between two models: for example
+   double **prop;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   double posprop;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   double  y2; /* in fractional years */
-    * progression in between and thus overestimating or underestimating according
+   int iagemin, iagemax;
-    * to the curvature of the survival function. If, for the same date, we
+   int first; /** to stop verbosity which is redirected to log file */
-    * 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
+   iagemin= (int) agemin;
-    * hypothesis. A more precise result, taking into account a more precise
+   iagemax= (int) agemax;
-    * curvature will be obtained if estepm is as small as stepm. */
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   j1=0;
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+   /*j=cptcoveff;*/
-      Look at hpijx to understand the reason of that which relies in memory size
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-      and note for a fixed period like estepm months */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   first=1;
-      survival function given by stepm (the optimization length). Unfortunately it
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-      means that if the survival funtion is printed only each two years of age and if
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       j1++;*/
-      results. So we changed our mind and took the option of the best precision.
-   */
+       for (i=1; i<=nlstate; i++)
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+         for(m=iagemin; m <= iagemax+3; m++)
+           prop[i][m]=0.0;
-   /* If stepm=6 months */
-   /* nhstepm age range expressed in number of stepm */
+       for (i=1; i<=imx; i++) { /* Each individual */
-   agelim=AGESUP;
+         bool=1;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         if  (cptcovn>0) {
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+           for (z1=1; z1<=cptcoveff; z1++)
-   /* if (stepm >= YEARM) hstepm=1;*/
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+               bool=0;
+         }
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if (bool==1) {
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               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 (age=bage; age<=fage; age ++){
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+                 prop[s[m][i]][iagemax+3] += weight[i];
+               }
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             }
+           } /* end selection of waves */
-     /* Computing  Variances of health expectancies */
+         }
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+       }
-        decrease memory allocation */
+       for(i=iagemin; i <= iagemax+3; i++){
-     for(theta=1; theta <=npar; theta++){
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-       for(i=1; i<=npar; i++){
+           posprop += prop[jk][i];
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         }
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-       }
+         for(jk=1; jk <=nlstate ; jk++){
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+           if( i <=  iagemax){
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-       for(j=1; j<= nlstate; j++){
+             } else{
-         for(i=1; i<=nlstate; i++){
+               if(first==1){
-           for(h=0; h<=nhstepm-1; h++){
+                 first=0;
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+                 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]);
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+               }
-           }
+             }
-         }
+           }
-       }
+         }/* end jk */
+       }/* end i */
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+     /*} *//* end i1 */
-         for(h=0; h<=nhstepm-1; h++){
+   } /* end j1 */
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         }
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-     }/* End theta */
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+ }  /* End of prevalence */
-     for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*nlstate;j++)
+ /************* Waves Concatenation ***************/
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+ {
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+      Death is a valid wave (if date is known).
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-         varhe[ij][ji][(int)age] =0.;
+      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.
-      printf("%d|",(int)age);fflush(stdout);
+      */
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
+   int i, mi, m;
-       for(k=0;k<=nhstepm-1;k++){
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+      double sum=0., jmean=0.;*/
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+   int first;
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+   int j, k=0,jk, ju, jl;
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+   double sum=0.;
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+   first=0;
-       }
+   jmin=100000;
-     }
+   jmax=-1;
+   jmean=0.;
-     /* Computing expectancies */
+   for(i=1; i<=imx; i++){
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     mi=0;
-     for(i=1; i<=nlstate;i++)
+     m=firstpass;
-       for(j=1; j<=nlstate;j++)
+     while(s[m][i] <= nlstate){
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+         mw[++mi][i]=m;
+       if(m >=lastpass)
-           /* 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]);*/
+         break;
+       else
-         }
+         m++;
+     }/* end while */
-     fprintf(ficresstdeij,"%3.0f",age );
+     if (s[m][i] > nlstate){
-     for(i=1; i<=nlstate;i++){
+       mi++;     /* Death is another wave */
-       eip=0.;
+       /* if(mi==0)  never been interviewed correctly before death */
-       vip=0.;
+          /* Only death is a correct wave */
-       for(j=1; j<=nlstate;j++){
+       mw[mi][i]=m;
-         eip += eij[i][j][(int)age];
+     }
-         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];
+     wav[i]=mi;
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+     if(mi==0){
-       }
+       nbwarn++;
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+       if(first==0){
-     }
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-     fprintf(ficresstdeij,"\n");
+         first=1;
+       }
-     fprintf(ficrescveij,"%3.0f",age );
+       if(first==1){
-     for(i=1; i<=nlstate;i++)
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-       for(j=1; j<=nlstate;j++){
+       }
-         cptj= (j-1)*nlstate+i;
+     } /* end mi==0 */
-         for(i2=1; i2<=nlstate;i2++)
+   } /* End individuals */
-           for(j2=1; j2<=nlstate;j2++){
-             cptj2= (j2-1)*nlstate+i2;
+   for(i=1; i<=imx; i++){
-             if(cptj2 <= cptj)
+     for(mi=1; mi<wav[i];mi++){
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+       if (stepm <=0)
-           }
+         dh[mi][i]=1;
-       }
+       else{
-     fprintf(ficrescveij,"\n");
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+           if (agedc[i] < 2*AGESUP) {
-   }
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+             else if(j<0){
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+               nberr++;
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+               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]);
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               j=1; /* Temporary Dangerous patch */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               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);
-   printf("\n");
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   fprintf(ficlog,"\n");
+               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);
+             }
-   free_vector(xm,1,npar);
+             k=k+1;
-   free_vector(xp,1,npar);
+             if (j >= jmax){
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+               jmax=j;
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+               ijmax=i;
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+             }
- }
+             if (j <= jmin){
+               jmin=j;
- /************ Variance ******************/
+               ijmin=i;
- 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[])
+             }
- {
+             sum=sum+j;
-   /* Variance of health expectancies */
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-   /* double **newm;*/
+           }
-   double **dnewm,**doldm;
+         }
-   double **dnewmp,**doldmp;
+         else{
-   int i, j, nhstepm, hstepm, h, nstepm ;
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-   int k, cptcode;
+ /*        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]); */
-   double *xp;
-   double **gp, **gm;  /* for var eij */
+           k=k+1;
-   double ***gradg, ***trgradg; /*for var eij */
+           if (j >= jmax) {
-   double **gradgp, **trgradgp; /* for var p point j */
+             jmax=j;
-   double *gpp, *gmp; /* for var p point j */
+             ijmax=i;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+           }
-   double ***p3mat;
+           else if (j <= jmin){
-   double age,agelim, hf;
+             jmin=j;
-   double ***mobaverage;
+             ijmin=i;
-   int theta;
+           }
-   char digit[4];
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-   char digitp[25];
+           /*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){
-   char fileresprobmorprev[FILENAMELENGTH];
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   if(popbased==1){
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-     if(mobilav!=0)
+           }
-       strcpy(digitp,"-populbased-mobilav-");
+           sum=sum+j;
-     else strcpy(digitp,"-populbased-nomobil-");
+         }
-   }
+         jk= j/stepm;
-   else
+         jl= j -jk*stepm;
-     strcpy(digitp,"-stablbased-");
+         ju= j -(jk+1)*stepm;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-   if (mobilav!=0) {
+           if(jl==0){
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             dh[mi][i]=jk;
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+             bh[mi][i]=0;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           }else{ /* We want a negative bias in order to only have interpolation ie
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                   * to avoid the price of an extra matrix product in likelihood */
-     }
+             dh[mi][i]=jk+1;
-   }
+             bh[mi][i]=ju;
+           }
-   strcpy(fileresprobmorprev,"prmorprev");
+         }else{
-   sprintf(digit,"%-d",ij);
+           if(jl <= -ju){
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+             dh[mi][i]=jk;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+             bh[mi][i]=jl;       /* bias is positive if real duration
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+                                  * is higher than the multiple of stepm and negative otherwise.
-   strcat(fileresprobmorprev,fileres);
+                                  */
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+           }
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+           else{
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+             dh[mi][i]=jk+1;
-   }
+             bh[mi][i]=ju;
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           }
+           if(dh[mi][i]==0){
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+             dh[mi][i]=1; /* At least one step */
-   pstamp(ficresprobmorprev);
+             bh[mi][i]=ju; /* At least one step */
-   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);
+             /*  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(ficresprobmorprev,"# Age cov=%-d",ij);
+           }
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+         } /* end if mle */
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+       }
-     for(i=1; i<=nlstate;i++)
+     } /* end wave */
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   }
-   }
+   jmean=sum/k;
-   fprintf(ficresprobmorprev,"\n");
+   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(ficgp,"\n# Routine varevsij");
+   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);
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+  }
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ /*********** Tricode ****************************/
- /*   } */
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ {
-   pstamp(ficresvij);
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   if(popbased==1)
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-   else
+    * nbcode[Tvar[j]][1]=
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   */
-   fprintf(ficresvij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-     for(j=1; j<=nlstate;j++)
+   int modmaxcovj=0; /* Modality max of covariates j */
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   int cptcode=0; /* Modality max of covariates j */
-   fprintf(ficresvij,"\n");
+   int modmincovj=0; /* Modality min of covariates j */
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   cptcoveff=0;
-   doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   /* Loop on covariates without age and products */
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-   gmp=vector(nlstate+1,nlstate+ndeath);
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+                                modality of this covariate Vj*/
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   if(estepm < stepm){
+                                     * If product of Vn*Vm, still boolean *:
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+                                     * 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   */
-   else  hstepm=estepm;
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   /* For example we decided to compute the life expectancy with the smallest unit */
+                                       modality of the nth covariate of individual i. */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       if (ij > modmaxcovj)
-      nhstepm is the number of hstepm from age to agelim
+         modmaxcovj=ij;
-      nstepm is the number of stepm from age to agelin.
+       else if (ij < modmincovj)
-      Look at hpijx to understand the reason of that which relies in memory size
+         modmincovj=ij;
-      and note for a fixed period like k years */
+       if ((ij < -1) && (ij > NCOVMAX)){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-      survival function given by stepm (the optimization length). Unfortunately it
+         exit(1);
-      means that if the survival funtion is printed every two years of age and if
+       }else
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-      results. So we changed our mind and took the option of the best precision.
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   */
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       /* getting the maximum value of the modality of the covariate
-   agelim = AGESUP;
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+          female is 1, then modmaxcovj=1.*/
-     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 */
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     cptcode=modmaxcovj;
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     gp=matrix(0,nhstepm,1,nlstate);
+    /*for (i=0; i<=cptcode; i++) {*/
-     gm=matrix(0,nhstepm,1,nlstate);
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-     for(theta=1; theta <=npar; theta++){
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+       }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-       }
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     } /* Ndum[-1] number of undefined modalities */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-       if (popbased==1) {
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-         if(mobilav ==0){
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-           for(i=1; i<=nlstate;i++)
+        modmincovj=3; modmaxcovj = 7;
-             prlim[i][i]=probs[(int)age][i][ij];
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
-         }else{ /* mobilav */
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-           for(i=1; i<=nlstate;i++)
+        variables V1_1 and V1_2.
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+        nbcode[Tvar[j]][ij]=k;
-         }
+        nbcode[Tvar[j]][1]=0;
-       }
+        nbcode[Tvar[j]][2]=1;
+        nbcode[Tvar[j]][3]=2;
-       for(j=1; j<= nlstate; j++){
+     */
-         for(h=0; h<=nhstepm; h++){
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-         }
+         /*recode from 0 */
-       }
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-       /* This for computing probability of death (h=1 means
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-          computed over hstepm matrices product = hstepm*stepm months)
+                                      k is a modality. If we have model=V1+V1*sex
-          as a weighted average of prlim.
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-       */
+           ij++;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         }
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+         if (ij > ncodemax[j]) break;
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+       }  /* end of loop on */
-       }
+     } /* end of loop on modality */
-       /* end probability of death */
+   } /* 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<=npar; i++) /* Computes gradient x - delta */
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-       if (popbased==1) {
+    Ndum[ij]++;
-         if(mobilav ==0){
+  }
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+  ij=1;
-         }else{ /* mobilav */
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-           for(i=1; i<=nlstate;i++)
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-         }
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-       }
+      Tvaraff[ij]=i; /*For printing (unclear) */
+      ij++;
-       for(j=1; j<= nlstate; j++){
+    }else
-         for(h=0; h<=nhstepm; h++){
+        Tvaraff[ij]=0;
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+  }
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+  ij--;
-         }
+  cptcoveff=ij; /*Number of total covariates*/
-       }
-       /* This for computing probability of death (h=1 means
+ }
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
+ /*********** Health Expectancies ****************/
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+ {
-       /* end probability of death */
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm;
-       for(j=1; j<= nlstate; j++) /* vareij */
+   int nhstepma, nstepma; /* Decreasing with age */
-         for(h=0; h<=nhstepm; h++){
+   double age, agelim, hf;
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   double ***p3mat;
-         }
+   double eip;
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   pstamp(ficreseij);
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   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");
+   for(i=1; i<=nlstate;i++){
-     } /* End theta */
+     for(j=1; j<=nlstate;j++){
+       fprintf(ficreseij," e%1d%1d ",i,j);
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+     }
+     fprintf(ficreseij," e%1d. ",i);
-     for(h=0; h<=nhstepm; h++) /* veij */
+   }
-       for(j=1; j<=nlstate;j++)
+   fprintf(ficreseij,"\n");
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   if(estepm < stepm){
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       for(theta=1; theta <=npar; theta++)
+   }
-         trgradgp[j][theta]=gradgp[theta][j];
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     for(i=1;i<=nlstate;i++)
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-       for(j=1;j<=nlstate;j++)
+    * progression in between and thus overestimating or underestimating according
-         vareij[i][j][(int)age] =0.;
+    * 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
-     for(h=0;h<=nhstepm;h++){
+    * to compare the new estimate of Life expectancy with the same linear
-       for(k=0;k<=nhstepm;k++){
+    * hypothesis. A more precise result, taking into account a more precise
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+    * curvature will be obtained if estepm is as small as stepm. */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for(i=1;i<=nlstate;i++)
+   /* For example we decided to compute the life expectancy with the smallest unit */
-           for(j=1;j<=nlstate;j++)
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+      nhstepm is the number of hstepm from age to agelim
-       }
+      nstepm is the number of stepm from age to agelin.
-     }
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
-     /* pptj */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      survival function given by stepm (the optimization length). Unfortunately it
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+      means that if the survival funtion is printed only each two years of age and if
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+      results. So we changed our mind and took the option of the best precision.
-         varppt[j][i]=doldmp[j][i];
+   */
-     /* end ppptj */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   agelim=AGESUP;
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-     if (popbased==1) {
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-       if(mobilav ==0){
-         for(i=1; i<=nlstate;i++)
+ /* nhstepm age range expressed in number of stepm */
-           prlim[i][i]=probs[(int)age][i][ij];
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       }else{ /* mobilav */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         for(i=1; i<=nlstate;i++)
+   /* if (stepm >= YEARM) hstepm=1;*/
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       }
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     }
+   for (age=bage; age<=fage; age ++){
-     /* This for computing probability of death (h=1 means
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-        as a weighted average of prlim.
+     /* if (stepm >= YEARM) hstepm=1;*/
-     */
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+     /* If stepm=6 months */
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-     }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     /* end probability of death */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       for(i=1; i<=nlstate;i++){
+     printf("%d|",(int)age);fflush(stdout);
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       }
-     }
+     /* Computing expectancies */
-     fprintf(ficresprobmorprev,"\n");
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
-     fprintf(ficresvij,"%.0f ",age );
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-     for(i=1; i<=nlstate;i++)
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+           /* 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(ficresvij,"\n");
+         }
-     free_matrix(gp,0,nhstepm,1,nlstate);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+     fprintf(ficreseij,"%3.0f",age );
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     for(i=1; i<=nlstate;i++){
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+       eip=0;
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for(j=1; j<=nlstate;j++){
-   } /* End age */
+         eip +=eij[i][j][(int)age];
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+       }
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+       fprintf(ficreseij,"%9.4f", eip );
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+     }
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     fprintf(ficreseij,"\n");
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   }
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   printf("\n");
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   fprintf(ficlog,"\n");
-   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));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   /*  fprintf(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);
+ {
- */
+   /* Covariances of health expectancies eij and of total life expectancies according
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+    to initial status i, ei. .
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   free_vector(xp,1,npar);
+   int nhstepma, nstepma; /* Decreasing with age */
-   free_matrix(doldm,1,nlstate,1,nlstate);
+   double age, agelim, hf;
-   free_matrix(dnewm,1,nlstate,1,npar);
+   double ***p3matp, ***p3matm, ***varhe;
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double **dnewm,**doldm;
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   double *xp, *xm;
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double **gp, **gm;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double ***gradg, ***trgradg;
-   fclose(ficresprobmorprev);
+   int theta;
-   fflush(ficgp);
-   fflush(fichtm);
+   double eip, vip;
- }  /* end varevsij */
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
- /************ Variance of prevlim ******************/
+   xp=vector(1,npar);
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+   xm=vector(1,npar);
- {
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   /* Variance of prevalence limit */
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
+   pstamp(ficresstdeij);
-   double **dnewm,**doldm;
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   int i, j, nhstepm, hstepm;
+   fprintf(ficresstdeij,"# Age");
-   int k, cptcode;
+   for(i=1; i<=nlstate;i++){
-   double *xp;
+     for(j=1; j<=nlstate;j++)
-   double *gp, *gm;
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   double **gradg, **trgradg;
+     fprintf(ficresstdeij," e%1d. ",i);
-   double age,agelim;
+   }
-   int theta;
+   fprintf(ficresstdeij,"\n");
-   pstamp(ficresvpl);
+   pstamp(ficrescveij);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficrescveij,"# Age");
    for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     for(j=1; j<=nlstate;j++){
-   fprintf(ficresvpl,"\n");
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
-   xp=vector(1,npar);
+         for(j2=1; j2<=nlstate;j2++){
-   dnewm=matrix(1,nlstate,1,npar);
+           cptj2= (j2-1)*nlstate+i2;
-   doldm=matrix(1,nlstate,1,nlstate);
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-   hstepm=1*YEARM; /* Every year of age */
+         }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     }
-   agelim = AGESUP;
+   fprintf(ficrescveij,"\n");
-   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(estepm < stepm){
-     if (stepm >= YEARM) hstepm=1;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   }
-     gradg=matrix(1,npar,1,nlstate);
+   else  hstepm=estepm;
-     gp=vector(1,nlstate);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     gm=vector(1,nlstate);
+    * 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
-     for(theta=1; theta <=npar; theta++){
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+    * progression in between and thus overestimating or underestimating according
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+    * 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
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+    * to compare the new estimate of Life expectancy with the same linear
-       for(i=1;i<=nlstate;i++)
+    * hypothesis. A more precise result, taking into account a more precise
-         gp[i] = prlim[i][i];
+    * curvature will be obtained if estepm is as small as stepm. */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      nhstepm is the number of hstepm from age to agelim
-       for(i=1;i<=nlstate;i++)
+      nstepm is the number of stepm from age to agelin.
-         gm[i] = prlim[i][i];
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
-       for(i=1;i<=nlstate;i++)
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+      survival function given by stepm (the optimization length). Unfortunately it
-     } /* End theta */
+      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
-     trgradg =matrix(1,nlstate,1,npar);
+      results. So we changed our mind and took the option of the best precision.
+   */
-     for(j=1; j<=nlstate;j++)
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       for(theta=1; theta <=npar; theta++)
-         trgradg[j][theta]=gradg[theta][j];
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
-     for(i=1;i<=nlstate;i++)
+   agelim=AGESUP;
-       varpl[i][(int)age] =0.;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   /* if (stepm >= YEARM) hstepm=1;*/
-     for(i=1;i<=nlstate;i++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficresvpl,"%.0f ",age );
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(i=1; i<=nlstate;i++)
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     fprintf(ficresvpl,"\n");
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     free_vector(gp,1,nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     free_vector(gm,1,nlstate);
-     free_matrix(gradg,1,npar,1,nlstate);
+   for (age=bage; age<=fage; age ++){
-     free_matrix(trgradg,1,nlstate,1,npar);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   } /* End age */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
-   free_vector(xp,1,npar);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+     /* If stepm=6 months */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
- }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
- /************ Variance of one-step probabilities  ******************/
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- 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[])
- {
+     /* Computing  Variances of health expectancies */
-   int i, j=0,  i1, k1, l1, t, tj;
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   int k2, l2, j1,  z1;
+        decrease memory allocation */
-   int k=0,l, cptcode;
+     for(theta=1; theta <=npar; theta++){
-   int first=1, first1;
+       for(i=1; i<=npar; i++){
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   double **dnewm,**doldm;
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-   double *xp;
+       }
-   double *gp, *gm;
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   double **gradg, **trgradg;
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   double **mu;
-   double age,agelim, cov[NCOVMAX];
+       for(j=1; j<= nlstate; j++){
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+         for(i=1; i<=nlstate; i++){
-   int theta;
+           for(h=0; h<=nhstepm-1; h++){
-   char fileresprob[FILENAMELENGTH];
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   char fileresprobcov[FILENAMELENGTH];
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   char fileresprobcor[FILENAMELENGTH];
+           }
+         }
-   double ***varpij;
+       }
-   strcpy(fileresprob,"prob");
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-   strcat(fileresprob,fileres);
+         for(h=0; h<=nhstepm-1; h++){
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-     printf("Problem with resultfile: %s\n", fileresprob);
+         }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+     }/* End theta */
-   }
-   strcpy(fileresprobcov,"probcov");
-   strcat(fileresprobcov,fileres);
+     for(h=0; h<=nhstepm-1; h++)
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+       for(j=1; j<=nlstate*nlstate;j++)
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+         for(theta=1; theta <=npar; theta++)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   }
-   strcpy(fileresprobcor,"probcor");
-   strcat(fileresprobcor,fileres);
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+         varhe[ij][ji][(int)age] =0.;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+      printf("%d|",(int)age);fflush(stdout);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+      for(h=0;h<=nhstepm-1;h++){
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+       for(k=0;k<=nhstepm-1;k++){
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   pstamp(ficresprob);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   fprintf(ficresprob,"# Age");
+       }
-   pstamp(ficresprobcov);
+     }
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+     /* Computing expectancies */
-   pstamp(ficresprobcor);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+     for(i=1; i<=nlstate;i++)
-   fprintf(ficresprobcor,"# Age");
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+         }
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+     fprintf(ficresstdeij,"%3.0f",age );
-  /* fprintf(ficresprob,"\n");
+     for(i=1; i<=nlstate;i++){
-   fprintf(ficresprobcov,"\n");
+       eip=0.;
-   fprintf(ficresprobcor,"\n");
+       vip=0.;
-  */
+       for(j=1; j<=nlstate;j++){
-  xp=vector(1,npar);
+         eip += eij[i][j][(int)age];
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+       }
-   first=1;
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   fprintf(ficgp,"\n# Routine varprob");
+     }
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     fprintf(ficresstdeij,"\n");
-   fprintf(fichtm,"\n");
+     fprintf(ficrescveij,"%3.0f",age );
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+     for(i=1; i<=nlstate;i++)
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+       for(j=1; j<=nlstate;j++){
-   file %s<br>\n",optionfilehtmcov);
+         cptj= (j-1)*nlstate+i;
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+         for(i2=1; i2<=nlstate;i2++)
- and drawn. It helps understanding how is the covariance between two incidences.\
+           for(j2=1; j2<=nlstate;j2++){
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+             cptj2= (j2-1)*nlstate+i2;
-   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(cptj2 <= cptj)
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+           }
- standard deviations wide on each axis. <br>\
+       }
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+     fprintf(ficrescveij,"\n");
-  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");
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-   cov[1]=1;
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-   tj=cptcoveff;
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   j1=0;
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   for(t=1; t<=tj;t++){
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(i1=1; i1<=ncodemax[t];i1++){
+   printf("\n");
-       j1++;
+   fprintf(ficlog,"\n");
-       if  (cptcovn>0) {
-         fprintf(ficresprob, "\n#********** Variable ");
+   free_vector(xm,1,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   free_vector(xp,1,npar);
-         fprintf(ficresprob, "**********\n#\n");
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-         fprintf(ficresprobcov, "**********\n#\n");
+ }
-         fprintf(ficgp, "\n#********** Variable ");
+ /************ Variance ******************/
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
-         fprintf(ficgp, "**********\n#\n");
+ {
+   /* Variance of health expectancies */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+   /* double **newm;*/
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   int movingaverage();
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   double **dnewm,**doldm;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   double **dnewmp,**doldmp;
-         fprintf(ficresprobcor, "**********\n#");
+   int i, j, nhstepm, hstepm, h, nstepm ;
-       }
+   int k;
+   double *xp;
-       for (age=bage; age<=fage; age ++){
+   double **gp, **gm;  /* for var eij */
-         cov[2]=age;
+   double ***gradg, ***trgradg; /*for var eij */
-         for (k=1; k<=cptcovn;k++) {
+   double **gradgp, **trgradgp; /* for var p point j */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   double *gpp, *gmp; /* for var p point j */
-         }
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   double ***p3mat;
-         for (k=1; k<=cptcovprod;k++)
+   double age,agelim, hf;
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   double ***mobaverage;
+   int theta;
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   char digit[4];
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   char digitp[25];
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   char fileresprobmorprev[FILENAMELENGTH];
-         for(theta=1; theta <=npar; theta++){
+   if(popbased==1){
-           for(i=1; i<=npar; i++)
+     if(mobilav!=0)
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+       strcpy(digitp,"-populbased-mobilav-");
+     else strcpy(digitp,"-populbased-nomobil-");
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   }
+   else
-           k=0;
+     strcpy(digitp,"-stablbased-");
-           for(i=1; i<= (nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+   if (mobilav!=0) {
-               k=k+1;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               gp[k]=pmmij[i][j];
+     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);
+     }
-           for(i=1; i<=npar; i++)
+   }
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   strcpy(fileresprobmorprev,"prmorprev");
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   sprintf(digit,"%-d",ij);
-           k=0;
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-           for(i=1; i<=(nlstate); i++){
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-             for(j=1; j<=(nlstate+ndeath);j++){
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-               k=k+1;
+   strcat(fileresprobmorprev,fileres);
-               gm[k]=pmmij[i][j];
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-             }
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-           }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   }
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-         }
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-           for(theta=1; theta <=npar; theta++)
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-             trgradg[j][theta]=gradg[theta][j];
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+     for(i=1; i<=nlstate;i++)
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   }
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   fprintf(ficresprobmorprev,"\n");
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   fprintf(ficgp,"\n# Routine varevsij");
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   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");
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ /*   } */
-         k=0;
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         for(i=1; i<=(nlstate); i++){
+   pstamp(ficresvij);
-           for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-             k=k+1;
+   if(popbased==1)
-             mu[k][(int) age]=pmmij[i][j];
+     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
-         }
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   fprintf(ficresvij,"# Age");
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   for(i=1; i<=nlstate;i++)
-             varpij[i][j][(int)age] = doldm[i][j];
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-         /*printf("\n%d ",(int)age);
+   fprintf(ficresvij,"\n");
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   xp=vector(1,npar);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   dnewm=matrix(1,nlstate,1,npar);
-           }*/
+   doldm=matrix(1,nlstate,1,nlstate);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-         fprintf(ficresprob,"\n%d ",(int)age);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+   gmp=vector(nlstate+1,nlstate+ndeath);
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+   if(estepm < stepm){
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         }
+   }
-         i=0;
+   else  hstepm=estepm;
-         for (k=1; k<=(nlstate);k++){
+   /* For example we decided to compute the life expectancy with the smallest unit */
-           for (l=1; l<=(nlstate+ndeath);l++){
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-             i=i++;
+      nhstepm is the number of hstepm from age to agelim
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+      nstepm is the number of stepm from age to agelin.
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-             for (j=1; j<=i;j++){
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+      survival function given by stepm (the optimization length). Unfortunately it
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+      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.
-         }/* end of loop for state */
+   */
-       } /* end of loop for age */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim = AGESUP;
-       /* Confidence intervalle of pij  */
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       /*
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         fprintf(ficgp,"\nset noparametric;unset label");
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         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);
+     gp=matrix(0,nhstepm,1,nlstate);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+     gm=matrix(0,nhstepm,1,nlstate);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       */
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       first1=1;
+       }
-       for (k2=1; k2<=(nlstate);k2++){
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
+       if (popbased==1) {
-           for (k1=1; k1<=(nlstate);k1++){
+         if(mobilav ==0){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+           for(i=1; i<=nlstate;i++)
-               if(l1==k1) continue;
+             prlim[i][i]=probs[(int)age][i][ij];
-               i=(k1-1)*(nlstate+ndeath)+l1;
+         }else{ /* mobilav */
-               if(i<=j) continue;
+           for(i=1; i<=nlstate;i++)
-               for (age=bage; age<=fage; age ++){
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-                 if ((int)age %5==0){
+         }
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+       }
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+       for(j=1; j<= nlstate; j++){
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+         for(h=0; h<=nhstepm; h++){
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-                   c12=cv12/sqrt(v1*v2);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-                   /* Computing eigen value of matrix of covariance */
+         }
-                   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.;
+       /* This for computing probability of death (h=1 means
-                   /* Eigen vectors */
+          computed over hstepm matrices product = hstepm*stepm months)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+          as a weighted average of prlim.
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+       */
-                   v21=(lc1-v1)/cv12*v11;
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                   v12=-v21;
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-                   v22=v11;
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-                   tnalp=v21/v11;
+       }
-                   if(first1==1){
+       /* end probability of death */
-                     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);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-                   }
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-                   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);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-                   /*printf(fignu*/
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+       if (popbased==1) {
-                   if(first==1){
+         if(mobilav ==0){
-                     first=0;
+           for(i=1; i<=nlstate;i++)
-                     fprintf(ficgp,"\nset parametric;unset label");
+             prlim[i][i]=probs[(int)age][i][ij];
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+         }else{ /* mobilav */
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+           for(i=1; i<=nlstate;i++)
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+         }
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+       }
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         for(h=0; h<=nhstepm; h++){
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+         }
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+       }
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+       /* This for computing probability of death (h=1 means
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+          computed over hstepm matrices product = hstepm*stepm months)
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+          as a weighted average of prlim.
-                   }else{
+       */
-                     first=0;
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-                     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",\
+       /* end probability of death */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+       for(j=1; j<= nlstate; j++) /* vareij */
-                   }/* if first */
+         for(h=0; h<=nhstepm; h++){
-                 } /* age mod 5 */
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-               } /* end loop age */
+         }
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-               first=1;
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-             } /*l12 */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-           } /* k12 */
+       }
-         } /*l1 */
-       }/* k1 */
+     } /* End theta */
-     } /* loop covariates */
-   }
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+     for(h=0; h<=nhstepm; h++) /* veij */
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+       for(j=1; j<=nlstate;j++)
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+         for(theta=1; theta <=npar; theta++)
-   free_vector(xp,1,npar);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   fclose(ficresprob);
-   fclose(ficresprobcov);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-   fclose(ficresprobcor);
+       for(theta=1; theta <=npar; theta++)
-   fflush(ficgp);
+         trgradgp[j][theta]=gradgp[theta][j];
-   fflush(fichtmcov);
- }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     for(i=1;i<=nlstate;i++)
- /******************* Printing html file ***********/
+       for(j=1;j<=nlstate;j++)
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+         vareij[i][j][(int)age] =0.;
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     for(h=0;h<=nhstepm;h++){
-                   int popforecast, int estepm ,\
+       for(k=0;k<=nhstepm;k++){
-                   double jprev1, double mprev1,double anprev1, \
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-                   double jprev2, double mprev2,double anprev2){
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-   int jj1, k1, i1, cpt;
+         for(i=1;i<=nlstate;i++)
+           for(j=1;j<=nlstate;j++)
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+       }
- </ul>");
+     }
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+     /* pptj */
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-    fprintf(fichtm,"\
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-    fprintf(fichtm,"\
+         varppt[j][i]=doldmp[j][i];
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+     /* end ppptj */
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+     /*  x centered again */
-    fprintf(fichtm,"\
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-  - (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): \
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-    <a href=\"%s\">%s</a> <br>\n",
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+     if (popbased==1) {
-    fprintf(fichtm,"\
+       if(mobilav ==0){
-  - Population projections by age and states: \
+         for(i=1; i<=nlstate;i++)
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+           prlim[i][i]=probs[(int)age][i][ij];
+       }else{ /* mobilav */
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-  m=cptcoveff;
+       }
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+     }
-  jj1=0;
+     /* This for computing probability of death (h=1 means
-  for(k1=1; k1<=m;k1++){
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-    for(i1=1; i1<=ncodemax[k1];i1++){
+        as a weighted average of prlim.
-      jj1++;
+     */
-      if (cptcovn > 0) {
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     }
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     /* end probability of death */
-      }
-      /* Pij */
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-      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> \
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-      /* Quasi-incidences */
+       for(i=1; i<=nlstate;i++){
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+       }
- <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 */
+     fprintf(ficresprobmorprev,"\n");
-        for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+     fprintf(ficresvij,"%.0f ",age );
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+     for(i=1; i<=nlstate;i++)
-        }
+       for(j=1; j<=nlstate;j++){
-      for(cpt=1; cpt<=nlstate;cpt++) {
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-         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> \
+       }
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+     fprintf(ficresvij,"\n");
-      }
+     free_matrix(gp,0,nhstepm,1,nlstate);
-    } /* end i1 */
+     free_matrix(gm,0,nhstepm,1,nlstate);
-  }/* End k1 */
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-  fprintf(fichtm,"</ul>");
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   } /* End age */
-  fprintf(fichtm,"\
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-  fprintf(fichtm,"\
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-  fprintf(fichtm,"\
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-  fprintf(fichtm,"\
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-  - 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): \
+   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);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   /*  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);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+ */
-  fprintf(fichtm,"\
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-    <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   free_vector(xp,1,npar);
-  fprintf(fichtm,"\
+   free_matrix(doldm,1,nlstate,1,nlstate);
-  - 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",
+   free_matrix(dnewm,1,nlstate,1,npar);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-  fprintf(fichtm,"\
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-  - 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",
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  fprintf(fichtm,"\
+   fclose(ficresprobmorprev);
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   fflush(ficgp);
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   fflush(fichtm);
+ }  /* end varevsij */
- /*  if(popforecast==1) fprintf(fichtm,"\n */
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /************ Variance of prevlim ******************/
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
- /*      <br>",fileres,fileres,fileres,fileres); */
+ {
- /*  else  */
+   /* Variance of prevalence limit */
- /*    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); */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-  fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   double **dnewm,**doldm;
+   int i, j, nhstepm, hstepm;
-  m=cptcoveff;
+   double *xp;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   double *gp, *gm;
+   double **gradg, **trgradg;
-  jj1=0;
+   double age,agelim;
-  for(k1=1; k1<=m;k1++){
+   int theta;
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      jj1++;
+   pstamp(ficresvpl);
-      if (cptcovn > 0) {
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   fprintf(ficresvpl,"# Age");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   for(i=1; i<=nlstate;i++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       fprintf(ficresvpl," %1d-%1d",i,i);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fprintf(ficresvpl,"\n");
-      }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   xp=vector(1,npar);
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   dnewm=matrix(1,nlstate,1,npar);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   doldm=matrix(1,nlstate,1,nlstate);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-      }
+   hstepm=1*YEARM; /* Every year of age */
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
- health expectancies in states (1) and (2): %s%d.png<br>\
+   agelim = AGESUP;
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-    } /* end i1 */
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-  }/* End k1 */
+     if (stepm >= YEARM) hstepm=1;
-  fprintf(fichtm,"</ul>");
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-  fflush(fichtm);
+     gradg=matrix(1,npar,1,nlstate);
- }
+     gp=vector(1,nlstate);
+     gm=vector(1,nlstate);
- /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-   char dirfileres[132],optfileres[132];
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+       }
-   int ng;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+       for(i=1;i<=nlstate;i++)
- /*     printf("Problem with file %s",optionfilegnuplot); */
+         gp[i] = prlim[i][i];
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- /*   } */
+       for(i=1; i<=npar; i++) /* Computes gradient */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   /*#ifdef windows */
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+       for(i=1;i<=nlstate;i++)
-     /*#endif */
+         gm[i] = prlim[i][i];
-   m=pow(2,cptcoveff);
+       for(i=1;i<=nlstate;i++)
-   strcpy(dirfileres,optionfilefiname);
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-   strcpy(optfileres,"vpl");
+     } /* End theta */
-  /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     trgradg =matrix(1,nlstate,1,npar);
-    for (k1=1; k1<= m ; k1 ++) {
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+     for(j=1; j<=nlstate;j++)
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+       for(theta=1; theta <=npar; theta++)
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+         trgradg[j][theta]=gradg[theta][j];
- set ylabel \"Probability\" \n\
- set ter png small\n\
+     for(i=1;i<=nlstate;i++)
- set size 0.65,0.65\n\
+       varpl[i][(int)age] =0.;
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-      for (i=1; i<= nlstate ; i ++) {
+     for(i=1;i<=nlstate;i++)
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+     fprintf(ficresvpl,"%.0f ",age );
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+     for(i=1; i<=nlstate;i++)
-      for (i=1; i<= nlstate ; i ++) {
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+     fprintf(ficresvpl,"\n");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+     free_vector(gp,1,nlstate);
-      }
+     free_vector(gm,1,nlstate);
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+     free_matrix(gradg,1,npar,1,nlstate);
-      for (i=1; i<= nlstate ; i ++) {
+     free_matrix(trgradg,1,nlstate,1,npar);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   } /* End age */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+   free_vector(xp,1,npar);
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+   free_matrix(doldm,1,nlstate,1,npar);
-    }
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   }
-   /*2 eme*/
+ }
-   for (k1=1; k1<= m ; k1 ++) {
+ /************ Variance of one-step probabilities  ******************/
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+ {
+   int i, j=0,  k1, l1, tj;
-     for (i=1; i<= nlstate+1 ; i ++) {
+   int k2, l2, j1,  z1;
-       k=2*i;
+   int k=0, l;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   int first=1, first1, first2;
-       for (j=1; j<= nlstate+1 ; j ++) {
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   double **dnewm,**doldm;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   double *xp;
-       }
+   double *gp, *gm;
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+   double **gradg, **trgradg;
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+   double **mu;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   double age, cov[NCOVMAX+1];
-       for (j=1; j<= nlstate+1 ; j ++) {
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   int theta;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   char fileresprob[FILENAMELENGTH];
-       }
+   char fileresprobcov[FILENAMELENGTH];
-       fprintf(ficgp,"\" t\"\" w l 0,");
+   char fileresprobcor[FILENAMELENGTH];
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+   double ***varpij;
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   strcpy(fileresprob,"prob");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   strcat(fileresprob,fileres);
-       }
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+     printf("Problem with resultfile: %s\n", fileresprob);
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-     }
+   }
-   }
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
-   /*3eme*/
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-   for (k1=1; k1<= m ; k1 ++) {
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+   }
-       /*       k=2+nlstate*(2*cpt-2); */
+   strcpy(fileresprobcor,"probcor");
-       k=2+(nlstate+1)*(cpt-1);
+   strcat(fileresprobcor,fileres);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-       fprintf(ficgp,"set ter png small\n\
+     printf("Problem with resultfile: %s\n", fileresprobcor);
- set size 0.65,0.65\n\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+   }
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
-       */
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-       for (i=1; i< nlstate ; i ++) {
+   fprintf(ficresprob,"# Age");
-         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);
+   pstamp(ficresprobcov);
-         /*      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);*/
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   fprintf(ficresprobcov,"# Age");
-       }
+   pstamp(ficresprobcor);
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-     }
+   fprintf(ficresprobcor,"# Age");
-   }
-   /* CV preval stable (period) */
+   for(i=1; i<=nlstate;i++)
-   for (k1=1; k1<= m ; k1 ++) {
+     for(j=1; j<=(nlstate+ndeath);j++){
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       k=3;
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+     }
- set ter png small\nset size 0.65,0.65\n\
+  /* fprintf(ficresprob,"\n");
- unset log y\n\
+   fprintf(ficresprobcov,"\n");
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+   fprintf(ficresprobcor,"\n");
+  */
-       for (i=1; i< nlstate ; i ++)
+   xp=vector(1,npar);
-         fprintf(ficgp,"+$%d",k+i+1);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-       l=3+(nlstate+ndeath)*cpt;
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+   first=1;
-       for (i=1; i< nlstate ; i ++) {
+   fprintf(ficgp,"\n# Routine varprob");
-         l=3+(nlstate+ndeath)*cpt;
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-         fprintf(ficgp,"+$%d",l+i+1);
+   fprintf(fichtm,"\n");
-       }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-     }
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   }
+   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   /* proba elementaires */
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   for(i=1,jk=1; i <=nlstate; i++){
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     for(k=1; k <=(nlstate+ndeath); k++){
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-       if (k != i) {
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-         for(j=1; j <=ncovmodel; j++){
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+ standard deviations wide on each axis. <br>\
-           jk++;
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-           fprintf(ficgp,"\n");
+  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");
-       }
-     }
+   cov[1]=1;
-    }
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-      for(jk=1; jk <=m; jk++) {
+   j1=0;
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+   for(j1=1; j1<=tj;j1++){
-        if (ng==2)
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+     /*j1++;*/
-        else
+       if  (cptcovn>0) {
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+         fprintf(ficresprob, "\n#********** Variable ");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        i=1;
+         fprintf(ficresprob, "**********\n#\n");
-        for(k2=1; k2<=nlstate; k2++) {
+         fprintf(ficresprobcov, "\n#********** Variable ");
-          k3=i;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-          for(k=1; k<=(nlstate+ndeath); k++) {
+         fprintf(ficresprobcov, "**********\n#\n");
-            if (k != k2){
-              if(ng==2)
+         fprintf(ficgp, "\n#********** Variable ");
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-              else
+         fprintf(ficgp, "**********\n#\n");
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
-              for(j=3; j <=ncovmodel; j++) {
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-                  ij++;
-                }
+         fprintf(ficresprobcor, "\n#********** Variable ");
-                else
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         fprintf(ficresprobcor, "**********\n#");
-              }
+       }
-              fprintf(ficgp,")/(1");
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-              for(k1=1; k1 <=nlstate; k1++){
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-                ij=1;
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-                for(j=3; j <=ncovmodel; j++){
+       for (age=bage; age<=fage; age ++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+         cov[2]=age;
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         for (k=1; k<=cptcovn;k++) {
-                    ij++;
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-                  }
+                                                          * 1  1 1 1 1
-                  else
+                                                          * 2  2 1 1 1
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                                                          * 3  1 2 1 1
-                }
+                                                          */
-                fprintf(ficgp,")");
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-              }
+         }
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+         for (k=1; k<=cptcovprod;k++)
-              i=i+ncovmodel;
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-            }
-          } /* end k */
-        } /* end k2 */
+         for(theta=1; theta <=npar; theta++){
-      } /* end jk */
+           for(i=1; i<=npar; i++)
-    } /* end ng */
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-    fflush(ficgp);
- }  /* end gnuplot */
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
- /*************** Moving average **************/
+           for(i=1; i<= (nlstate); i++){
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
-   int i, cpt, cptcod;
+               gp[k]=pmmij[i][j];
-   int modcovmax =1;
+             }
-   int mobilavrange, mob;
+           }
-   double age;
+           for(i=1; i<=npar; i++)
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-                            a covariate has 2 modalities */
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+           for(i=1; i<=(nlstate); i++){
-     if(mobilav==1) mobilavrange=5; /* default */
+             for(j=1; j<=(nlstate+ndeath);j++){
-     else mobilavrange=mobilav;
+               k=k+1;
-     for (age=bage; age<=fage; age++)
+               gm[k]=pmmij[i][j];
-       for (i=1; i<=nlstate;i++)
+             }
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+           }
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-     /* We keep the original values on the extreme ages bage, fage and for
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-        we use a 5 terms etc. until the borders are no more concerned.
+         }
-     */
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+           for(theta=1; theta <=npar; theta++)
-         for (i=1; i<=nlstate;i++){
+             trgradg[j][theta]=gradg[theta][j];
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-               }
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+         k=0;
-           }
+         for(i=1; i<=(nlstate); i++){
-         }
+           for(j=1; j<=(nlstate+ndeath);j++){
-       }/* end age */
+             k=k+1;
-     }/* end mob */
+             mu[k][(int) age]=pmmij[i][j];
-   }else return -1;
+           }
-   return 0;
+         }
- }/* End movingaverage */
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             varpij[i][j][(int)age] = doldm[i][j];
- /************** Forecasting ******************/
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+         /*printf("\n%d ",(int)age);
-   /* proj1, year, month, day of starting projection
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-      agemin, agemax range of age
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-      anproj2 year of en of projection (same day and month as proj1).
+           }*/
-   */
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+         fprintf(ficresprob,"\n%d ",(int)age);
-   int *popage;
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-   double agec; /* generic age */
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-   double *popeffectif,*popcount;
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-   double ***p3mat;
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-   double ***mobaverage;
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-   char fileresf[FILENAMELENGTH];
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-   agelim=AGESUP;
+         }
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         i=0;
+         for (k=1; k<=(nlstate);k++){
-   strcpy(fileresf,"f");
+           for (l=1; l<=(nlstate+ndeath);l++){
-   strcat(fileresf,fileres);
+             i++;
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+             for (j=1; j<=i;j++){
-   }
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+           }
+         }/* end of loop for state */
-   if (mobilav!=0) {
+       } /* end of loop for age */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-     }
-   }
+       /* Confidence intervalle of pij  */
+       /*
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+         fprintf(ficgp,"\nunset parametric;unset label");
-   if (stepm<=12) stepsize=1;
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   if(estepm < stepm){
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-   }
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-   else  hstepm=estepm;
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-   hstepm=hstepm/stepm;
+       */
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-                                fractional in yp1 */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-   anprojmean=yp;
+       first1=1;first2=2;
-   yp2=modf((yp1*12),&yp);
+       for (k2=1; k2<=(nlstate);k2++){
-   mprojmean=yp;
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-   yp1=modf((yp2*30.5),&yp);
+           if(l2==k2) continue;
-   jprojmean=yp;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-   if(jprojmean==0) jprojmean=1;
+           for (k1=1; k1<=(nlstate);k1++){
-   if(mprojmean==0) jprojmean=1;
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
+               if(l1==k1) continue;
-   i1=cptcoveff;
+               i=(k1-1)*(nlstate+ndeath)+l1;
-   if (cptcovn < 1){i1=1;}
+               if(i<=j) continue;
+               for (age=bage; age<=fage; age ++){
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
- /*            if (h==(int)(YEARM*yearp)){ */
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+                   c12=cv12/sqrt(v1*v2);
-       k=k+1;
+                   /* Computing eigen value of matrix of covariance */
-       fprintf(ficresf,"\n#******");
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-       for(j=1;j<=cptcoveff;j++) {
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                   if ((lc2 <0) || (lc1 <0) ){
-       }
+                     if(first2==1){
-       fprintf(ficresf,"******\n");
+                       first1=0;
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+                     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);
-       for(j=1; j<=nlstate+ndeath;j++){
+                     }
-         for(i=1; i<=nlstate;i++)
+                     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);
-           fprintf(ficresf," p%d%d",i,j);
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-         fprintf(ficresf," p.%d",j);
+                     /* lc2=fabs(lc2); */
-       }
+                   }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-         fprintf(ficresf,"\n");
+                   /* Eigen vectors */
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+                   v21=(lc1-v1)/cv12*v11;
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+                   v12=-v21;
-           nhstepm = nhstepm/hstepm;
+                   v22=v11;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                   tnalp=v21/v11;
-           oldm=oldms;savm=savms;
+                   if(first1==1){
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+                     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);
-           for (h=0; h<=nhstepm; h++){
+                   }
-             if (h*hstepm/YEARM*stepm ==yearp) {
+                   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(ficresf,"\n");
+                   /*printf(fignu*/
-               for(j=1;j<=cptcoveff;j++)
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+                   if(first==1){
-             }
+                     first=0;
-             for(j=1; j<=nlstate+ndeath;j++) {
+                     fprintf(ficgp,"\nset parametric;unset label");
-               ppij=0.;
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-               for(i=1; i<=nlstate;i++) {
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-                 if (mobilav==1)
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-                 else {
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-                 }
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                 if (h*hstepm/YEARM*stepm== yearp) {
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                     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);
-               } /* end i */
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-               if (h*hstepm/YEARM*stepm==yearp) {
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                 fprintf(ficresf," %.3f", ppij);
+                     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),\
-             }/* end j */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-           } /* end h */
+                   }else{
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                     first=0;
-         } /* end agec */
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-       } /* end yearp */
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-     } /* end cptcod */
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   } /* end  cptcov */
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
-   fclose(ficresf);
+                 } /* age mod 5 */
- }
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- /************** Forecasting *****not tested NB*************/
+               first=1;
- 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){
+             } /*l12 */
+           } /* k12 */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+         } /*l1 */
-   int *popage;
+       }/* k1 */
-   double calagedatem, agelim, kk1, kk2;
+       /* } */ /* loop covariates */
-   double *popeffectif,*popcount;
+   }
-   double ***p3mat,***tabpop,***tabpopprev;
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   double ***mobaverage;
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   char filerespop[FILENAMELENGTH];
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_vector(xp,1,npar);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprob);
-   agelim=AGESUP;
+   fclose(ficresprobcov);
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   fclose(ficresprobcor);
+   fflush(ficgp);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   fflush(fichtmcov);
+ }
-   strcpy(filerespop,"pop");
-   strcat(filerespop,fileres);
+ /******************* Printing html file ***********/
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+                   int lastpass, int stepm, int weightopt, char model[],\
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   }
+                   int popforecast, int estepm ,\
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+                   double jprev1, double mprev1,double anprev1, \
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   if (mobilav!=0) {
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ </ul>");
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-     }
+    fprintf(fichtm,"\
-   }
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+    fprintf(fichtm,"\
-   if (stepm<=12) stepsize=1;
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-   agelim=AGESUP;
+    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): \
-   hstepm=1;
+    <a href=\"%s\">%s</a> <br>\n",
-   hstepm=hstepm/stepm;
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
-   if (popforecast==1) {
+  - Population projections by age and states: \
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-     }
-     popage=ivector(0,AGESUP);
+  m=pow(2,cptcoveff);
-     popeffectif=vector(0,AGESUP);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-     popcount=vector(0,AGESUP);
+  jj1=0;
-     i=1;
+  for(k1=1; k1<=m;k1++){
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
-     imx=i;
+      if (cptcovn > 0) {
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   }
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      }
-       k=k+1;
+      /* Pij */
-       fprintf(ficrespop,"\n#******");
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-       for(j=1;j<=cptcoveff;j++) {
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      /* Quasi-incidences */
-       }
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-       fprintf(ficrespop,"******\n");
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-       fprintf(ficrespop,"# Age");
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+        /* Period (stable) prevalence in each health state */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
-       for (cpt=0; cpt<=0;cpt++) {
+ <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+        }
+      for(cpt=1; cpt<=nlstate;cpt++) {
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-           nhstepm = nhstepm/hstepm;
+      }
+    } /* end i1 */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  }/* End k1 */
-           oldm=oldms;savm=savms;
+  fprintf(fichtm,"</ul>");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           for (h=0; h<=nhstepm; h++){
+  fprintf(fichtm,"\
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               kk1=0.;kk2=0;
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-               for(i=1; i<=nlstate;i++) {
+  fprintf(fichtm,"\
-                 if (mobilav==1)
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-                 else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+  fprintf(fichtm,"\
-                 }
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               }
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-               if (h==(int)(calagedatem+12*cpt)){
+  fprintf(fichtm,"\
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+  - 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): \
-                   /*fprintf(ficrespop," %.3f", kk1);
+    <a href=\"%s\">%s</a> <br>\n</li>",
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-               }
+  fprintf(fichtm,"\
-             }
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
-             for(i=1; i<=nlstate;i++){
+    <a href=\"%s\">%s</a> <br>\n</li>",
-               kk1=0.;
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-                 for(j=1; j<=nlstate;j++){
+  fprintf(fichtm,"\
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-                 }
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+  fprintf(fichtm,"\
-             }
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+  fprintf(fichtm,"\
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-           }
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+ /*  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 */
-   /******/
+ /*      <br>",fileres,fileres,fileres,fileres); */
+ /*  else  */
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+  fflush(fichtm);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
+  m=pow(2,cptcoveff);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+  jj1=0;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+  for(k1=1; k1<=m;k1++){
-           for (h=0; h<=nhstepm; h++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+      jj1++;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+      if (cptcovn > 0) {
-             }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-             for(j=1; j<=nlstate+ndeath;j++) {
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-               kk1=0.;kk2=0;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-               for(i=1; i<=nlstate;i++) {
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+      }
-               }
+      for(cpt=1; cpt<=nlstate;cpt++) {
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-             }
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-           }
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      }
-         }
+      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\
-   }
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+    } /* end i1 */
-   if (popforecast==1) {
+  }/* End k1 */
-     free_ivector(popage,0,AGESUP);
+  fprintf(fichtm,"</ul>");
-     free_vector(popeffectif,0,AGESUP);
+  fflush(fichtm);
-     free_vector(popcount,0,AGESUP);
+ }
-   }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /******************* Gnuplot file **************/
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   fclose(ficrespop);
- } /* End of popforecast */
+   char dirfileres[132],optfileres[132];
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
- int fileappend(FILE *fichier, char *optionfich)
+   int ng=0;
- {
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     printf("Problem with file: %s\n", optionfich);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+ /*   } */
-     return (0);
-   }
+   /*#ifdef windows */
-   fflush(fichier);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   return (1);
+     /*#endif */
- }
+   m=pow(2,cptcoveff);
+   strcpy(dirfileres,optionfilefiname);
- /**************** function prwizard **********************/
+   strcpy(optfileres,"vpl");
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+  /* 1eme*/
- {
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-   /* Wizard to print covariance matrix template */
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-   char ca[32], cb[32], cc[32];
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-   int numlinepar;
+ set ylabel \"Probability\" \n\
+ set ter png small size 320, 240\n\
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   for(i=1; i <=nlstate; i++){
+      for (i=1; i<= nlstate ; i ++) {
-     jj=0;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-     for(j=1; j <=nlstate+ndeath; j++){
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-       if(j==i) continue;
+      }
-       jj++;
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+      for (i=1; i<= nlstate ; i ++) {
-       printf("%1d%1d",i,j);
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       fprintf(ficparo,"%1d%1d",i,j);
+        else fprintf(ficgp," %%*lf (%%*lf)");
-       for(k=1; k<=ncovmodel;k++){
+      }
-         /*        printf(" %lf",param[i][j][k]); */
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+      for (i=1; i<= nlstate ; i ++) {
-         printf(" 0.");
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         fprintf(ficparo," 0.");
+        else fprintf(ficgp," %%*lf (%%*lf)");
-       }
+      }
-       printf("\n");
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-       fprintf(ficparo,"\n");
+    }
-     }
+   }
-   }
+   /*2 eme*/
-   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   for (k1=1; k1<= m ; k1 ++) {
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-   for(i=1; i <=nlstate; i++){
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+     for (i=1; i<= nlstate+1 ; i ++) {
-       if(j==i) continue;
+       k=2*i;
-       jj++;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       fprintf(ficparo,"%1d%1d",i,j);
+       for (j=1; j<= nlstate+1 ; j ++) {
-       printf("%1d%1d",i,j);
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       fflush(stdout);
+         else fprintf(ficgp," %%*lf (%%*lf)");
-       for(k=1; k<=ncovmodel;k++){
+       }
-         /*      printf(" %le",delti3[i][j][k]); */
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-         printf(" 0.");
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-         fprintf(ficparo," 0.");
+       for (j=1; j<= nlstate+1 ; j ++) {
-       }
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       numlinepar++;
+         else fprintf(ficgp," %%*lf (%%*lf)");
-       printf("\n");
+       }
-       fprintf(ficparo,"\n");
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-     }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   }
+       for (j=1; j<= nlstate+1 ; j ++) {
-   printf("# Covariance matrix\n");
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
- /* # 121 Var(a12)\n\ */
+         else fprintf(ficgp," %%*lf (%%*lf)");
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+       }
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     }
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   }
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   /*3eme*/
-   fflush(stdout);
-   fprintf(ficparo,"# Covariance matrix\n");
+   for (k1=1; k1<= m ; k1 ++) {
-   /* # 121 Var(a12)\n\ */
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+       /*       k=2+nlstate*(2*cpt-2); */
-   /* #   ...\n\ */
+       k=2+(nlstate+1)*(cpt-1);
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-   for(itimes=1;itimes<=2;itimes++){
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-     jj=0;
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     for(i=1; i <=nlstate; i++){
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-       for(j=1; j <=nlstate+ndeath; j++){
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-         if(j==i) continue;
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for(k=1; k<=ncovmodel;k++){
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-           jj++;
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           ca[0]= k+'a'-1;ca[1]='\0';
-           if(itimes==1){
+       */
-             printf("#%1d%1d%d",i,j,k);
+       for (i=1; i< nlstate ; i ++) {
-             fprintf(ficparo,"#%1d%1d%d",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+i,cpt,i+1);
-           }else{
+         /*      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("%1d%1d%d",i,j,k);
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+       }
-             /*  printf(" %.5le",matcov[i][j]); */
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-           }
+     }
-           ll=0;
+   }
-           for(li=1;li <=nlstate; li++){
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+   /* CV preval stable (period) */
-               if(lj==li) continue;
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-               for(lk=1;lk<=ncovmodel;lk++){
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-                 ll++;
+       k=3;
-                 if(ll<=jj){
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-                   if(ll<jj){
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-                     if(itimes==1){
+ set ter png small size 320, 240\n\
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ unset log y\n\
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-                     }else{
+       for (i=1; i<= nlstate ; i ++){
-                       printf(" 0.");
+         if(i==1)
-                       fprintf(ficparo," 0.");
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-                     }
+         else
-                   }else{
+           fprintf(ficgp,", '' ");
-                     if(itimes==1){
+         l=(nlstate+ndeath)*(i-1)+1;
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+         for (j=1; j<= (nlstate-1) ; j ++)
-                     }else{
+           fprintf(ficgp,"+$%d",k+l+j);
-                       printf(" 0.");
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-                       fprintf(ficparo," 0.");
+       } /* nlstate */
-                     }
+       fprintf(ficgp,"\n");
-                   }
+     } /* end cpt state*/
-                 }
+   } /* end covariate */
-               } /* end lk */
-             } /* end lj */
+   /* proba elementaires */
-           } /* end li */
+   for(i=1,jk=1; i <=nlstate; i++){
-           printf("\n");
+     for(k=1; k <=(nlstate+ndeath); k++){
-           fprintf(ficparo,"\n");
+       if (k != i) {
-           numlinepar++;
+         for(j=1; j <=ncovmodel; j++){
-         } /* end k*/
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-       } /*end j */
+           jk++;
-     } /* end i */
+           fprintf(ficgp,"\n");
-   } /* end itimes */
+         }
+       }
- } /* end of prwizard */
+     }
- /******************* Gompertz Likelihood ******************************/
+    }
- double gompertz(double x[])
+   /*goto avoid;*/
- {
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   double A,B,L=0.0,sump=0.,num=0.;
+      for(jk=1; jk <=m; jk++) {
-   int i,n=0; /* n is the size of the sample */
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+        if (ng==2)
-   for (i=0;i<=imx-1 ; i++) {
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-     sump=sump+weight[i];
+        else
-     /*    sump=sump+1;*/
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     num=num+1;
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   }
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
+          k3=i;
-   /* for (i=0; i<=imx; i++)
+          for(k=1; k<=(nlstate+ndeath); k++) {
-      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+            if (k != k2){
+              if(ng==2)
-   for (i=1;i<=imx ; i++)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-     {
+              else
-       if (cens[i] == 1 && wav[i]>1)
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+              ij=1;/* To be checked else nbcode[0][0] wrong */
+              for(j=3; j <=ncovmodel; j++) {
-       if (cens[i] == 0 && wav[i]>1)
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+                /*        ij++; */
+                /* } */
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+                /* else */
-       if (wav[i] > 1 ) { /* ??? */
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-         L=L+A*weight[i];
+              }
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+              fprintf(ficgp,")/(1");
-       }
-     }
+              for(k1=1; k1 <=nlstate; k1++){
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+                ij=1;
+                for(j=3; j <=ncovmodel; j++){
-   return -2*L*num/sump;
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
- }
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
+                  /*   ij++; */
- /******************* Printing html file ***********/
+                  /* } */
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                  /* else */
-                   int lastpass, int stepm, int weightopt, char model[],\
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-                   int imx,  double p[],double **matcov,double agemortsup){
+                }
-   int i,k;
+                fprintf(ficgp,")");
+              }
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-   for (i=1;i<=2;i++)
+              i=i+ncovmodel;
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+            }
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+          } /* end k */
-   fprintf(fichtm,"</ul>");
+        } /* end k2 */
+      } /* end jk */
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+    } /* end ng */
+  /* avoid: */
-  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>");
+    fflush(ficgp);
+ }  /* end gnuplot */
-  for (k=agegomp;k<(agemortsup-2);k++)
-    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+ /*************** Moving average **************/
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-   fflush(fichtm);
- }
+   int i, cpt, cptcod;
+   int modcovmax =1;
- /******************* Gnuplot file **************/
+   int mobilavrange, mob;
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   double age;
-   char dirfileres[132],optfileres[132];
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+                            a covariate has 2 modalities */
-   int ng;
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-   /*#ifdef windows */
+     if(mobilav==1) mobilavrange=5; /* default */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     else mobilavrange=mobilav;
-     /*#endif */
+     for (age=bage; age<=fage; age++)
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-   strcpy(dirfileres,optionfilefiname);
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   strcpy(optfileres,"vpl");
+     /* We keep the original values on the extreme ages bage, fage and for
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+        we use a 5 terms etc. until the borders are no more concerned.
-   fprintf(ficgp, "set ter png small\n set log y\n");
+     */
-   fprintf(ficgp, "set size 0.65,0.65\n");
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+         for (i=1; i<=nlstate;i++){
- }
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+               }
- /***********************************************/
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
- /**************** Main Program *****************/
+           }
- /***********************************************/
+         }
+       }/* end age */
- int main(int argc, char *argv[])
+     }/* end mob */
- {
+   }else return -1;
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   return 0;
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+ }/* End movingaverage */
-   int linei, month, year,iout;
-   int jj, ll, li, lj, lk, imk;
-   int numlinepar=0; /* Current linenumber of parameter file */
+ /************** Forecasting ******************/
-   int itimes;
+ 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){
-   int NDIM=2;
+   /* proj1, year, month, day of starting projection
+      agemin, agemax range of age
-   char ca[32], cb[32], cc[32];
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-   char dummy[]="                         ";
+      anproj2 year of en of projection (same day and month as proj1).
-   /*  FILE *fichtm; *//* Html File */
+   */
-   /* FILE *ficgp;*/ /*Gnuplot File */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
-   struct stat info;
+   double agec; /* generic age */
-   double agedeb, agefin,hf;
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double *popeffectif,*popcount;
+   double ***p3mat;
-   double fret;
+   double ***mobaverage;
-   double **xi,tmp,delta;
+   char fileresf[FILENAMELENGTH];
-   double dum; /* Dummy variable */
+   agelim=AGESUP;
-   double ***p3mat;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   double ***mobaverage;
-   int *indx;
+   strcpy(fileresf,"f");
-   char line[MAXLINE], linepar[MAXLINE];
+   strcat(fileresf,fileres);
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-   char **bp, *tok, *val; /* pathtot */
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   int firstobs=1, lastobs=10;
+   }
-   int sdeb, sfin; /* Status at beginning and end */
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   int c,  h , cpt,l;
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   if (mobilav!=0) {
-   int mobilav=0,popforecast=0;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int hstepm, nhstepm;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   int agemortsup;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   float  sumlpop=0.;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   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, fage, age, agelim, agebase;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   double ftolpl=FTOL;
+   if (stepm<=12) stepsize=1;
-   double **prlim;
+   if(estepm < stepm){
-   double *severity;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   double ***param; /* Matrix of parameters */
+   }
-   double  *p;
+   else  hstepm=estepm;
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
+   hstepm=hstepm/stepm;
-   double *delti; /* Scale */
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-   double ***eij, ***vareij;
+                                fractional in yp1 */
-   double **varpl; /* Variances of prevalence limits by age */
+   anprojmean=yp;
-   double *epj, vepp;
+   yp2=modf((yp1*12),&yp);
-   double kk1, kk2;
+   mprojmean=yp;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   yp1=modf((yp2*30.5),&yp);
-   double **ximort;
+   jprojmean=yp;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   if(jprojmean==0) jprojmean=1;
-   int *dcwave;
+   if(mprojmean==0) jprojmean=1;
-   char z[1]="c", occ;
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   char *stratrunc;
-   int lstra;
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-   long total_usecs;
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
- /*   setlocale (LC_ALL, ""); */
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       k=k+1;
- /*   textdomain (PACKAGE); */
+       fprintf(ficresf,"\n#******");
- /*   setlocale (LC_CTYPE, ""); */
+       for(j=1;j<=cptcoveff;j++) {
- /*   setlocale (LC_MESSAGES, ""); */
+         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]]);
+       }
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       fprintf(ficresf,"******\n");
-   (void) gettimeofday(&start_time,&tzp);
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   curr_time=start_time;
+       for(j=1; j<=nlstate+ndeath;j++){
-   tm = *localtime(&start_time.tv_sec);
+         for(i=1; i<=nlstate;i++)
-   tmg = *gmtime(&start_time.tv_sec);
+           fprintf(ficresf," p%d%d",i,j);
-   strcpy(strstart,asctime(&tm));
+         fprintf(ficresf," p.%d",j);
+       }
- /*  printf("Localtime (at start)=%s",strstart); */
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
- /*  tp.tv_sec = tp.tv_sec +86400; */
+         fprintf(ficresf,"\n");
- /*  tm = *localtime(&start_time.tv_sec); */
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+         for (agec=fage; agec>=(ageminpar-1); agec--){
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
- /*   tp.tv_sec = mktime(&tmg); */
+           nhstepm = nhstepm/hstepm;
- /*   strt=asctime(&tmg); */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*   printf("Time(after) =%s",strstart);  */
+           oldm=oldms;savm=savms;
- /*  (void) time (&time_value);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
- *  tm = *localtime(&time_value);
+           for (h=0; h<=nhstepm; h++){
- *  strstart=asctime(&tm);
+             if (h*hstepm/YEARM*stepm ==yearp) {
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+               fprintf(ficresf,"\n");
- */
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   nberr=0; /* Number of errors and warnings */
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-   nbwarn=0;
+             }
-   getcwd(pathcd, size);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               ppij=0.;
-   printf("\n%s\n%s",version,fullversion);
+               for(i=1; i<=nlstate;i++) {
-   if(argc <=1){
+                 if (mobilav==1)
-     printf("\nEnter the parameter file name: ");
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-     fgets(pathr,FILENAMELENGTH,stdin);
+                 else {
-     i=strlen(pathr);
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-     if(pathr[i-1]=='\n')
+                 }
-       pathr[i-1]='\0';
+                 if (h*hstepm/YEARM*stepm== yearp) {
-    for (tok = pathr; tok != NULL; ){
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-       printf("Pathr |%s|\n",pathr);
+                 }
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+               } /* end i */
-       printf("val= |%s| pathr=%s\n",val,pathr);
+               if (h*hstepm/YEARM*stepm==yearp) {
-       strcpy (pathtot, val);
+                 fprintf(ficresf," %.3f", ppij);
-       if(pathr[0] == '\0') break; /* Dirty */
+               }
-     }
+             }/* end j */
-   }
+           } /* end h */
-   else{
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     strcpy(pathtot,argv[1]);
+         } /* end agec */
-   }
+       } /* end yearp */
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+     } /* end cptcod */
-   /*cygwin_split_path(pathtot,path,optionfile);
+   } /* end  cptcov */
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /* Split argv[0], imach program to get pathimach */
+   fclose(ficresf);
-   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);
+ /************** Forecasting *****not tested NB*************/
-  /*   strcpy(pathimach,argv[0]); */
+ 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){
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   int *popage;
-   chdir(path); /* Can be a relative path */
+   double calagedatem, agelim, kk1, kk2;
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   double *popeffectif,*popcount;
-     printf("Current directory %s!\n",pathcd);
+   double ***p3mat,***tabpop,***tabpopprev;
-   strcpy(command,"mkdir ");
+   double ***mobaverage;
-   strcat(command,optionfilefiname);
+   char filerespop[FILENAMELENGTH];
-   if((outcmd=system(command)) != 0){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     /* fclose(ficlog); */
+   agelim=AGESUP;
- /*     exit(1); */
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   }
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
- /*     perror("mkdir"); */
- /*   } */
+   strcpy(filerespop,"pop");
-   /*-------- arguments in the command line --------*/
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   /* Log file */
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   strcat(filelog, optionfilefiname);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   strcat(filelog,".log");    /* */
+   }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-     printf("Problem with logfile %s\n",filelog);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-     goto end;
-   }
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   if (mobilav!=0) {
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-  path=%s \n\
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-  optionfile=%s\n\
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-  optionfilext=%s\n\
+     }
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   }
-   printf("Local time (at start):%s",strstart);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+   if (stepm<=12) stepsize=1;
-   fflush(ficlog);
- /*   (void) gettimeofday(&curr_time,&tzp); */
+   agelim=AGESUP;
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   hstepm=1;
-   /* */
+   hstepm=hstepm/stepm;
-   strcpy(fileres,"r");
-   strcat(fileres, optionfilefiname);
+   if (popforecast==1) {
-   strcat(fileres,".txt");    /* Other files have txt extension */
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   /*---------arguments file --------*/
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+     }
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     popage=ivector(0,AGESUP);
-     printf("Problem with optionfile %s\n",optionfile);
+     popeffectif=vector(0,AGESUP);
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     popcount=vector(0,AGESUP);
-     fflush(ficlog);
-     goto end;
+     i=1;
-   }
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   strcpy(filereso,"o");
+   }
-   strcat(filereso,fileres);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-     printf("Problem with Output resultfile: %s\n", filereso);
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+       k=k+1;
-     fflush(ficlog);
+       fprintf(ficrespop,"\n#******");
-     goto end;
+       for(j=1;j<=cptcoveff;j++) {
-   }
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-   /* Reads comments: lines beginning with '#' */
+       fprintf(ficrespop,"******\n");
-   numlinepar=0;
+       fprintf(ficrespop,"# Age");
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-     ungetc(c,ficpar);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
+       for (cpt=0; cpt<=0;cpt++) {
-     puts(line);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   }
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   ungetc(c,ficpar);
+           nhstepm = nhstepm/hstepm;
-   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);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   numlinepar++;
+           oldm=oldms;savm=savms;
-   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);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   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);
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+           for (h=0; h<=nhstepm; h++){
-   fflush(ficlog);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   while((c=getc(ficpar))=='#' && c!= EOF){
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     ungetc(c,ficpar);
+             }
-     fgets(line, MAXLINE, ficpar);
+             for(j=1; j<=nlstate+ndeath;j++) {
-     numlinepar++;
+               kk1=0.;kk2=0;
-     puts(line);
+               for(i=1; i<=nlstate;i++) {
-     fputs(line,ficparo);
+                 if (mobilav==1)
-     fputs(line,ficlog);
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   }
+                 else {
-   ungetc(c,ficpar);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
-   covar=matrix(0,NCOVMAX,1,n);
+               if (h==(int)(calagedatem+12*cpt)){
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+               }
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+             }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+                 for(j=1; j<=nlstate;j++){
-   delti=delti3[1][1];
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+                 }
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+             }
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-     fclose (ficparo);
+           }
-     fclose (ficlog);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     goto end;
+         }
-     exit(0);
+       }
-   }
-   else if(mle==-3) {
+   /******/
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-     matcov=matrix(1,npar,1,npar);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   }
+           nhstepm = nhstepm/hstepm;
-   else{
-     /* Read guess parameters */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* Reads comments: lines beginning with '#' */
+           oldm=oldms;savm=savms;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-       ungetc(c,ficpar);
+           for (h=0; h<=nhstepm; h++){
-       fgets(line, MAXLINE, ficpar);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       numlinepar++;
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       puts(line);
+             }
-       fputs(line,ficparo);
+             for(j=1; j<=nlstate+ndeath;j++) {
-       fputs(line,ficlog);
+               kk1=0.;kk2=0;
-     }
+               for(i=1; i<=nlstate;i++) {
-     ungetc(c,ficpar);
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-     for(i=1; i <=nlstate; i++){
+             }
-       j=0;
+           }
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         if(jj==i) continue;
+         }
-         j++;
+       }
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+    }
-         if ((i1 != i) && (j1 != j)){
+   }
-           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 \
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           exit(1);
+   if (popforecast==1) {
-         }
+     free_ivector(popage,0,AGESUP);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+     free_vector(popeffectif,0,AGESUP);
-         if(mle==1)
+     free_vector(popcount,0,AGESUP);
-           printf("%1d%1d",i,j);
+   }
-         fprintf(ficlog,"%1d%1d",i,j);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         for(k=1; k<=ncovmodel;k++){
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-           fscanf(ficpar," %lf",&param[i][j][k]);
+   fclose(ficrespop);
-           if(mle==1){
+ } /* End of popforecast */
-             printf(" %lf",param[i][j][k]);
-             fprintf(ficlog," %lf",param[i][j][k]);
+ int fileappend(FILE *fichier, char *optionfich)
-           }
+ {
-           else
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-             fprintf(ficlog," %lf",param[i][j][k]);
+     printf("Problem with file: %s\n", optionfich);
-           fprintf(ficparo," %lf",param[i][j][k]);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-         }
+     return (0);
-         fscanf(ficpar,"\n");
+   }
-         numlinepar++;
+   fflush(fichier);
-         if(mle==1)
+   return (1);
-           printf("\n");
+ }
-         fprintf(ficlog,"\n");
-         fprintf(ficparo,"\n");
-       }
+ /**************** function prwizard **********************/
-     }
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-     fflush(ficlog);
+ {
-     p=param[1][1];
+   /* Wizard to print covariance matrix template */
-     /* Reads comments: lines beginning with '#' */
+   char ca[32], cb[32];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-       ungetc(c,ficpar);
+   int numlinepar;
-       fgets(line, MAXLINE, ficpar);
-       numlinepar++;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-       puts(line);
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-       fputs(line,ficparo);
+   for(i=1; i <=nlstate; i++){
-       fputs(line,ficlog);
+     jj=0;
-     }
+     for(j=1; j <=nlstate+ndeath; j++){
-     ungetc(c,ficpar);
+       if(j==i) continue;
+       jj++;
-     for(i=1; i <=nlstate; i++){
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       printf("%1d%1d",i,j);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       fprintf(ficparo,"%1d%1d",i,j);
-         if ((i1-i)*(j1-j)!=0){
+       for(k=1; k<=ncovmodel;k++){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         /*        printf(" %lf",param[i][j][k]); */
-           exit(1);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-         }
+         printf(" 0.");
-         printf("%1d%1d",i,j);
+         fprintf(ficparo," 0.");
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       }
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       printf("\n");
-         for(k=1; k<=ncovmodel;k++){
+       fprintf(ficparo,"\n");
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+     }
-           printf(" %le",delti3[i][j][k]);
+   }
-           fprintf(ficparo," %le",delti3[i][j][k]);
+   printf("# Scales (for hessian or gradient estimation)\n");
-           fprintf(ficlog," %le",delti3[i][j][k]);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-         }
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-         fscanf(ficpar,"\n");
+   for(i=1; i <=nlstate; i++){
-         numlinepar++;
+     jj=0;
-         printf("\n");
+     for(j=1; j <=nlstate+ndeath; j++){
-         fprintf(ficparo,"\n");
+       if(j==i) continue;
-         fprintf(ficlog,"\n");
+       jj++;
-       }
+       fprintf(ficparo,"%1d%1d",i,j);
-     }
+       printf("%1d%1d",i,j);
-     fflush(ficlog);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
-     delti=delti3[1][1];
+         /*      printf(" %le",delti3[i][j][k]); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+         fprintf(ficparo," 0.");
+       }
-     /* Reads comments: lines beginning with '#' */
+       numlinepar++;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       printf("\n");
-       ungetc(c,ficpar);
+       fprintf(ficparo,"\n");
-       fgets(line, MAXLINE, ficpar);
+     }
-       numlinepar++;
+   }
-       puts(line);
+   printf("# Covariance matrix\n");
-       fputs(line,ficparo);
+ /* # 121 Var(a12)\n\ */
-       fputs(line,ficlog);
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     }
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     ungetc(c,ficpar);
+ /* # 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\ */
-     matcov=matrix(1,npar,1,npar);
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     for(i=1; i <=npar; i++){
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-       fscanf(ficpar,"%s",&str);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-       if(mle==1)
+   fflush(stdout);
-         printf("%s",str);
+   fprintf(ficparo,"# Covariance matrix\n");
-       fprintf(ficlog,"%s",str);
+   /* # 121 Var(a12)\n\ */
-       fprintf(ficparo,"%s",str);
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-       for(j=1; j <=i; j++){
+   /* #   ...\n\ */
-         fscanf(ficpar," %le",&matcov[i][j]);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-         if(mle==1){
-           printf(" %.5le",matcov[i][j]);
+   for(itimes=1;itimes<=2;itimes++){
-         }
+     jj=0;
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     for(i=1; i <=nlstate; i++){
-         fprintf(ficparo," %.5le",matcov[i][j]);
+       for(j=1; j <=nlstate+ndeath; j++){
-       }
+         if(j==i) continue;
-       fscanf(ficpar,"\n");
+         for(k=1; k<=ncovmodel;k++){
-       numlinepar++;
+           jj++;
-       if(mle==1)
+           ca[0]= k+'a'-1;ca[1]='\0';
-         printf("\n");
+           if(itimes==1){
-       fprintf(ficlog,"\n");
+             printf("#%1d%1d%d",i,j,k);
-       fprintf(ficparo,"\n");
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-     }
+           }else{
-     for(i=1; i <=npar; i++)
+             printf("%1d%1d%d",i,j,k);
-       for(j=i+1;j<=npar;j++)
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-         matcov[i][j]=matcov[j][i];
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
-     if(mle==1)
+           ll=0;
-       printf("\n");
+           for(li=1;li <=nlstate; li++){
-     fprintf(ficlog,"\n");
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
-     fflush(ficlog);
+               for(lk=1;lk<=ncovmodel;lk++){
+                 ll++;
-     /*-------- Rewriting parameter file ----------*/
+                 if(ll<=jj){
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+                   if(ll<jj){
-     strcat(rfileres,".");    /* */
+                     if(itimes==1){
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+                     }else{
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+                       printf(" 0.");
-     }
+                       fprintf(ficparo," 0.");
-     fprintf(ficres,"#%s\n",version);
+                     }
-   }    /* End of mle != -3 */
+                   }else{
+                     if(itimes==1){
-   /*-------- data file ----------*/
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-   if((fic=fopen(datafile,"r"))==NULL)    {
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+                     }else{
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+                       printf(" 0.");
-   }
+                       fprintf(ficparo," 0.");
+                     }
-   n= lastobs;
+                   }
-   severity = vector(1,maxwav);
+                 }
-   outcome=imatrix(1,maxwav+1,1,n);
+               } /* end lk */
-   num=lvector(1,n);
+             } /* end lj */
-   moisnais=vector(1,n);
+           } /* end li */
-   annais=vector(1,n);
+           printf("\n");
-   moisdc=vector(1,n);
+           fprintf(ficparo,"\n");
-   andc=vector(1,n);
+           numlinepar++;
-   agedc=vector(1,n);
+         } /* end k*/
-   cod=ivector(1,n);
+       } /*end j */
-   weight=vector(1,n);
+     } /* end i */
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   } /* end itimes */
-   mint=matrix(1,maxwav,1,n);
-   anint=matrix(1,maxwav,1,n);
+ } /* end of prwizard */
-   s=imatrix(1,maxwav+1,1,n);
+ /******************* Gompertz Likelihood ******************************/
-   tab=ivector(1,NCOVMAX);
+ double gompertz(double x[])
-   ncodemax=ivector(1,8);
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
-   i=1;
+   int i,n=0; /* n is the size of the sample */
-   linei=0;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+   for (i=0;i<=imx-1 ; i++) {
-     linei=linei+1;
+     sump=sump+weight[i];
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+     /*    sump=sump+1;*/
-       if(line[j] == '\t')
+     num=num+1;
-         line[j] = ' ';
+   }
-     }
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       ;
+   /* 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]);*/
-     line[j+1]=0;  /* Trims blanks at end of line */
-     if(line[0]=='#'){
+   for (i=1;i<=imx ; i++)
-       fprintf(ficlog,"Comment line\n%s\n",line);
+     {
-       printf("Comment line\n%s\n",line);
+       if (cens[i] == 1 && wav[i]>1)
-       continue;
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-     }
+       if (cens[i] == 0 && wav[i]>1)
-     for (j=maxwav;j>=1;j--){
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-       cutv(stra, strb,line,' ');
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-       errno=0;
-       lval=strtol(strb,&endptr,10);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+       if (wav[i] > 1 ) { /* ??? */
-       if( strb[0]=='\0' || (*endptr != '\0')){
+         L=L+A*weight[i];
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+         /*      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]);*/
-         exit(1);
+       }
-       }
+     }
-       s[j][i]=lval;
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       strcpy(line,stra);
-       cutv(stra, strb,line,' ');
+   return -2*L*num/sump;
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
-       }
-       else  if(iout=sscanf(strb,"%s.") != 0){
+ #ifdef GSL
-         month=99;
+ /******************* Gompertz_f Likelihood ******************************/
-         year=9999;
+ double gompertz_f(const gsl_vector *v, void *params)
-       }else{
+ {
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+   double A,B,LL=0.0,sump=0.,num=0.;
-         exit(1);
+   double *x= (double *) v->data;
-       }
+   int i,n=0; /* n is the size of the sample */
-       anint[j][i]= (double) year;
-       mint[j][i]= (double)month;
+   for (i=0;i<=imx-1 ; i++) {
-       strcpy(line,stra);
+     sump=sump+weight[i];
-     } /* ENd Waves */
+     /*    sump=sump+1;*/
+     num=num+1;
-     cutv(stra, strb,line,' ');
+   }
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+   /* for (i=0; i<=imx; i++)
-       month=99;
+      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]);*/
-       year=9999;
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     }else{
+   for (i=1;i<=imx ; i++)
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+     {
-       exit(1);
+       if (cens[i] == 1 && wav[i]>1)
-     }
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-     andc[i]=(double) year;
-     moisdc[i]=(double) month;
+       if (cens[i] == 0 && wav[i]>1)
-     strcpy(line,stra);
+         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);
-     cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     }
+       if (wav[i] > 1 ) { /* ??? */
-     else  if(iout=sscanf(strb,"%s.") != 0){
+         LL=LL+A*weight[i];
-       month=99;
+         /*      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]);*/
-       year=9999;
+       }
-     }else{
+     }
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
-       exit(1);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     }
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-     annais[i]=(double)(year);
-     moisnais[i]=(double)(month);
+   return -2*LL*num/sump;
-     strcpy(line,stra);
+ }
+ #endif
-     cutv(stra, strb,line,' ');
-     errno=0;
+ /******************* Printing html file ***********/
-     dval=strtod(strb,&endptr);
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-     if( strb[0]=='\0' || (*endptr != '\0')){
+                   int lastpass, int stepm, int weightopt, char model[],\
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+                   int imx,  double p[],double **matcov,double agemortsup){
-       exit(1);
+   int i,k;
-     }
-     weight[i]=dval;
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     strcpy(line,stra);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
-     for (j=ncovcol;j>=1;j--){
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-       cutv(stra, strb,line,' ');
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-       errno=0;
+   fprintf(fichtm,"</ul>");
-       lval=strtol(strb,&endptr,10);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
-         exit(1);
+  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(lval <-1 || lval >1){
+  for (k=agegomp;k<(agemortsup-2);k++)
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+    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]);
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n \
+   fflush(fichtm);
-  build V1=0 V2=0 for the reference value (1),\n \
+ }
-         V1=1 V2=0 for (2) \n \
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+ /******************* Gnuplot file **************/
-  output of IMaCh is often meaningless.\n \
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-  Exiting.\n",lval,linei, i,line,j);
-         exit(1);
+   char dirfileres[132],optfileres[132];
-       }
-       covar[j][i]=(double)(lval);
+   int ng;
-       strcpy(line,stra);
-     }
-     lstra=strlen(stra);
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+     /*#endif */
-       stratrunc = &(stra[lstra-9]);
-       num[i]=atol(stratrunc);
-     }
+   strcpy(dirfileres,optionfilefiname);
-     else
+   strcpy(optfileres,"vpl");
-       num[i]=atol(stra);
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-       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;}*/
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-     i=i+1;
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-   } /* End loop reading  data */
-   fclose(fic);
+ }
-   /* printf("ii=%d", ij);
-      scanf("%d",i);*/
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-   imx=i-1; /* Number of individuals */
+ {
-   /* for (i=1; i<=imx; i++){
+   /*-------- data file ----------*/
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   FILE *fic;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   char dummy[]="                         ";
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+   int i=0, j=0, n=0;
-     }*/
+   int linei, month, year,iout;
-    /*  for (i=1; i<=imx; i++){
+   char line[MAXLINE], linetmp[MAXLINE];
-      if (s[4][i]==9)  s[4][i]=-1;
+   char stra[MAXLINE], strb[MAXLINE];
-      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]));}*/
+   char *stratrunc;
+   int lstra;
-   /* for (i=1; i<=imx; i++) */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+   if((fic=fopen(datafile,"r"))==NULL)    {
-      else weight[i]=1;*/
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-   /* Calculation of the number of parameters from char model */
+   }
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
-   Tprod=ivector(1,15);
+   i=1;
-   Tvaraff=ivector(1,15);
+   linei=0;
-   Tvard=imatrix(1,15,1,2);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-   Tage=ivector(1,15);
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+       if(line[j] == '\t')
-     j=0, j1=0, k1=1, k2=1;
+         line[j] = ' ';
-     j=nbocc(model,'+'); /* j=Number of '+' */
+     }
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-     cptcovn=j+1;
+       ;
-     cptcovprod=j1; /*Number of products */
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
-     strcpy(modelsav,model);
+     if(line[0]=='#'){
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+       fprintf(ficlog,"Comment line\n%s\n",line);
-       printf("Error. Non available option model=%s ",model);
+       printf("Comment line\n%s\n",line);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       continue;
-       goto end;
+     }
-     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     strcpy(line, linetmp);
-     /* This loop fills the array Tvar from the string 'model'.*/
-     for(i=(j+1); i>=1;i--){
+     for (j=maxwav;j>=1;j--){
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+       cutv(stra, strb, line, ' ');
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       if(strb[0]=='.') { /* Missing status */
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         lval=-1;
-       /*scanf("%d",i);*/
+       }else{
-       if (strchr(strb,'*')) {  /* Model includes a product */
+         errno=0;
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+         lval=strtol(strb,&endptr,10);
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-           cptcovprod--;
+         if( strb[0]=='\0' || (*endptr != '\0')){
-           cutv(strb,stre,strd,'V');
+           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);
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+           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);
-           cptcovage++;
+           return 1;
-             Tage[cptcovage]=i;
+         }
-             /*printf("stre=%s ", stre);*/
+       }
-         }
+       s[j][i]=lval;
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+       strcpy(line,stra);
-           cutv(strb,stre,strc,'V');
+       cutv(stra, strb,line,' ');
-           Tvar[i]=atoi(stre);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-           cptcovage++;
+       }
-           Tage[cptcovage]=i;
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-         }
+         month=99;
-         else {  /* Age is not in the model */
+         year=9999;
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+       }else{
-           Tvar[i]=ncovcol+k1;
+         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);
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+         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);
-           Tprod[k1]=i;
+         return 1;
-           Tvard[k1][1]=atoi(strc); /* m*/
+       }
-           Tvard[k1][2]=atoi(stre); /* n */
+       anint[j][i]= (double) year;
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+       mint[j][i]= (double)month;
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+       strcpy(line,stra);
-           for (k=1; k<=lastobs;k++)
+     } /* ENd Waves */
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           k1++;
+     cutv(stra, strb,line,' ');
-           k2=k2+2;
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-         }
+     }
-       }
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-       else { /* no more sum */
+       month=99;
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       year=9999;
-        /*  scanf("%d",i);*/
+     }else{
-       cutv(strd,strc,strb,'V');
+       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);
-       Tvar[i]=atoi(strc);
+         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;
-       strcpy(modelsav,stra);
+     }
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+     andc[i]=(double) year;
-         scanf("%d",i);*/
+     moisdc[i]=(double) month;
-     } /* end of loop + */
+     strcpy(line,stra);
-   } /* end model */
+     cutv(stra, strb,line,' ');
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+     }
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+       month=99;
-   printf("cptcovprod=%d ", cptcovprod);
+       year=9999;
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-   scanf("%d ",i);*/
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
-     /*  if(mle==1){*/
+     }
-   if (weightopt != 1) { /* Maximisation without weights*/
+     if (year==9999) {
-     for(i=1;i<=n;i++) weight[i]=1.0;
+       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);
-     /*-calculation of age at interview from date of interview and age at death -*/
+         return 1;
-   agev=matrix(1,maxwav,1,imx);
+     }
-   for (i=1; i<=imx; i++) {
+     annais[i]=(double)(year);
-     for(m=2; (m<= maxwav); m++) {
+     moisnais[i]=(double)(month);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+     strcpy(line,stra);
-         anint[m][i]=9999;
-         s[m][i]=-1;
+     cutv(stra, strb,line,' ');
-       }
+     errno=0;
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+     dval=strtod(strb,&endptr);
-         nberr++;
+     if( strb[0]=='\0' || (*endptr != '\0')){
-         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);
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-         fprintf(ficlog,"Error! 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(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-         s[m][i]=-1;
+       fflush(ficlog);
-       }
+       return 1;
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+     }
-         nberr++;
+     weight[i]=dval;
-         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]);
+     strcpy(line,stra);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+     for (j=ncovcol;j>=1;j--){
-       }
+       cutv(stra, strb,line,' ');
-     }
+       if(strb[0]=='.') { /* Missing status */
-   }
+         lval=-1;
+       }else{
-   for (i=1; i<=imx; i++)  {
+         errno=0;
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+         lval=strtol(strb,&endptr,10);
-     for(m=firstpass; (m<= lastpass); m++){
+         if( strb[0]=='\0' || (*endptr != '\0')){
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+           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);
-         if (s[m][i] >= nlstate+1) {
+           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);
-           if(agedc[i]>0)
+           return 1;
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+         }
-               agev[m][i]=agedc[i];
+       }
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+       if(lval <-1 || lval >1){
-             else {
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-               if ((int)andc[i]!=9999){
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-                 nbwarn++;
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+  For example, for multinomial values like 1, 2 and 3,\n \
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+  build V1=0 V2=0 for the reference value (1),\n \
-                 agev[m][i]=-1;
+         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);
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-                                  years but with the precision of a month */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+  For example, for multinomial values like 1, 2 and 3,\n \
-             agev[m][i]=1;
+  build V1=0 V2=0 for the reference value (1),\n \
-           else if(agev[m][i] <agemin){
+         V1=1 V2=0 for (2) \n \
-             agemin=agev[m][i];
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+  output of IMaCh is often meaningless.\n \
-           }
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-           else if(agev[m][i] >agemax){
+         return 1;
-             agemax=agev[m][i];
+       }
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+       covar[j][i]=(double)(lval);
-           }
+       strcpy(line,stra);
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+     }
-           /*     agev[m][i] = age[i]+2*m;*/
+     lstra=strlen(stra);
-         }
-         else { /* =9 */
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-           agev[m][i]=1;
+       stratrunc = &(stra[lstra-9]);
-           s[m][i]=-1;
+       num[i]=atol(stratrunc);
-         }
+     }
-       }
+     else
-       else /*= 0 Unknown */
+       num[i]=atol(stra);
-         agev[m][i]=1;
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-     }
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-   }
+     i=i+1;
-   for (i=1; i<=imx; i++)  {
+   } /* End loop reading  data */
-     for(m=firstpass; (m<=lastpass); m++){
-       if (s[m][i] > (nlstate+ndeath)) {
+   *imax=i-1; /* Number of individuals */
-         nberr++;
+   fclose(fic);
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+   return (0);
-         goto end;
+   /* endread: */
-       }
+     printf("Exiting readdata: ");
-     }
+     fclose(fic);
-   }
+     return (1);
-   /*for (i=1; i<=imx; i++){
-   for (m=firstpass; (m<lastpass); m++){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
- }
+ void removespace(char *str) {
+   char *p1 = str, *p2 = str;
- }*/
+   do
+     while (*p2 == ' ')
+       p2++;
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   while (*p1++ == *p2++);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+ }
-   agegomp=(int)agemin;
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-   free_vector(severity,1,maxwav);
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-   free_imatrix(outcome,1,maxwav+1,1,n);
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-   free_vector(moisnais,1,n);
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-   free_vector(annais,1,n);
+    * - cptcovage number of covariates with age*products =2
-   /* free_matrix(mint,1,maxwav,1,n);
+    * - cptcovs number of simple covariates
-      free_matrix(anint,1,maxwav,1,n);*/
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
-   free_vector(moisdc,1,n);
+    *     which is a new column after the 9 (ncovcol) variables.
-   free_vector(andc,1,n);
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-   wav=ivector(1,imx);
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+  */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+ {
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   int i, j, k, ks;
+   int  j1, k1, k2;
-   /* Concatenates waves */
+   char modelsav[80];
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-   Tcode=ivector(1,100);
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-   ncodemax[1]=1;
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+                   /* including age products which are counted in cptcovage.
-                                  the estimations*/
+                   * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-   h=0;
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-   m=pow(2,cptcoveff);
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+     strcpy(modelsav,model);
-   for(k=1;k<=cptcoveff; k++){
+     if (strstr(model,"AGE") !=0){
-     for(i=1; i <=(m/pow(2,k));i++){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-       for(j=1; j <= ncodemax[k]; j++){
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+       return 1;
-           h++;
+     }
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+     if (strstr(model,"v") !=0){
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-         }
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-       }
+       return 1;
      }
-   }
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+     /*   Design
-      codtab[1][2]=1;codtab[2][2]=2; */
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-   /* for(i=1; i <=m ;i++){
+      *  <          ncovcol=8                >
-      for(k=1; k <=cptcovn; k++){
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+      *   k=  1    2      3       4     5       6      7        8
-      }
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-      printf("\n");
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-      }
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-      scanf("%d",i);*/
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-   /*------------ gnuplot -------------*/
+      *  Tage[++cptcovage]=k
-   strcpy(optionfilegnuplot,optionfilefiname);
+      *       if products, new covar are created after ncovcol with k1
-   if(mle==-3)
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-     strcat(optionfilegnuplot,"-mort");
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-   strcat(optionfilegnuplot,".gp");
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-     printf("Problem with file %s",optionfilegnuplot);
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-   }
+      *  <          ncovcol=8                >
-   else{
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-     fprintf(ficgp,"\n# %s\n", version);
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-     fprintf(ficgp,"set missing 'NaNq'\n");
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-   }
+      * p Tprod[1]@2={                         6, 5}
-   /*  fclose(ficgp);*/
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-   /*--------- index.htm --------*/
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+      *How to reorganize?
-   if(mle==-3)
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-     strcat(optionfilehtm,"-mort");
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-   strcat(optionfilehtm,".htm");
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+      * Struct []
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+      */
-   }
+     /* This loop fills the array Tvar from the string 'model'.*/
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-   strcat(optionfilehtmcov,"-cov.htm");
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-   }
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-   else{
+     /*  k=1 Tvar[1]=2 (from V2) */
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     /*  k=5 Tvar[5] */
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     /* for (k=1; k<=cptcovn;k++) { */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+     /*  } */
-   }
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     /*
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+         Tvar[k]=0;
- \n\
+     cptcovage=0;
- <hr  size=\"2\" color=\"#EC5E5E\">\
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-  <ul><li><h4>Parameter files</h4>\n\
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+       /*scanf("%d",i);*/
-  - Date and time at start: %s</ul>\n",\
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-           fileres,fileres,\
+           /* covar is not filled and then is empty */
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+           cptcovprod--;
-   fflush(fichtm);
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-   strcpy(pathr,path);
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-   strcat(pathr,optionfilefiname);
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           /*printf("stre=%s ", stre);*/
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+           cptcovprod--;
-      and prints on file fileres'p'. */
+           cutl(stre,strb,strc,'V');
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+           Tvar[k]=atoi(stre);
+           cptcovage++;
-   fprintf(fichtm,"\n");
+           Tage[cptcovage]=k;
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           cptcovn++;
-           imx,agemin,agemax,jmin,jmax,jmean);
+           cptcovprodnoage++;k1++;
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                                   because this model-covariate is a construction we invent a new column
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+                                   ncovcol + k1
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+           k2=k2+2;
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+           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) */
-   if (mle==-3){
+           for (i=1; i<=lastobs;i++){
-     ximort=matrix(1,NDIM,1,NDIM);
+             /* Computes the new covariate which is a product of
-     cens=ivector(1,n);
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-     ageexmed=vector(1,n);
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-     agecens=vector(1,n);
+           }
-     dcwave=ivector(1,n);
+         } /* End age is not in the model */
+       } /* End if model includes a product */
-     for (i=1; i<=imx; i++){
+       else { /* no more sum */
-       dcwave[i]=-1;
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       for (m=firstpass; m<=lastpass; m++)
+        /*  scanf("%d",i);*/
-         if (s[m][i]>nlstate) {
+         cutl(strd,strc,strb,'V');
-           dcwave[i]=m;
+         ks++; /**< Number of simple covariates */
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+         cptcovn++;
-           break;
+         Tvar[k]=atoi(strd);
-         }
+       }
-     }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-     for (i=1; i<=imx; i++) {
+         scanf("%d",i);*/
-       if (wav[i]>0){
+     } /* end of loop + */
-         ageexmed[i]=agev[mw[1][i]][i];
+   } /* end model */
-         j=wav[i];
-         agecens[i]=1.;
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-         if (ageexmed[i]> 1 && wav[i] > 0){
-           agecens[i]=agev[mw[j][i]][i];
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-           cens[i]= 1;
+   printf("cptcovprod=%d ", cptcovprod);
-         }else if (ageexmed[i]< 1)
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-           cens[i]= -1;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   scanf("%d ",i);*/
-           cens[i]=0 ;
-       }
-       else cens[i]=-1;
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-     }
+   /*endread:*/
+     printf("Exiting decodemodel: ");
-     for (i=1;i<=NDIM;i++) {
+     return (1);
-       for (j=1;j<=NDIM;j++)
+ }
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
-     }
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
-     p[1]=0.0268; p[NDIM]=0.083;
+   int i, m;
-     /*printf("%lf %lf", p[1], p[2]);*/
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-     strcpy(filerespow,"pow-mort");
+         anint[m][i]=9999;
-     strcat(filerespow,fileres);
+         s[m][i]=-1;
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       }
-       printf("Problem with resultfile: %s\n", filerespow);
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         *nberr = *nberr + 1;
-     }
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+         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);
-     /*  for (i=1;i<=nlstate;i++)
+         s[m][i]=-1;
-         for(j=1;j<=nlstate+ndeath;j++)
+       }
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-     */
+         (*nberr)++;
-     fprintf(ficrespow,"\n");
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-     fclose(ficrespow);
+       }
+     }
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   }
-     for(i=1; i <=NDIM; i++)
+   for (i=1; i<=imx; i++)  {
-       for(j=i+1;j<=NDIM;j++)
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-         matcov[i][j]=matcov[j][i];
+     for(m=firstpass; (m<= lastpass); m++){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-     printf("\nCovariance matrix\n ");
+         if (s[m][i] >= nlstate+1) {
-     for(i=1; i <=NDIM; i++) {
+           if(agedc[i]>0){
-       for(j=1;j<=NDIM;j++){
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
-         printf("%f ",matcov[i][j]);
+               agev[m][i]=agedc[i];
-       }
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-       printf("\n ");
+             }else {
-     }
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-     for (i=1;i<=NDIM;i++)
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+                 agev[m][i]=-1;
+               }
-     lsurv=vector(1,AGESUP);
+             }
-     lpop=vector(1,AGESUP);
+           } /* agedc > 0 */
-     tpop=vector(1,AGESUP);
+         }
-     lsurv[agegomp]=100000;
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                  years but with the precision of a month */
-     for (k=agegomp;k<=AGESUP;k++) {
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-       agemortsup=k;
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+             agev[m][i]=1;
-     }
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
-     for (k=agegomp;k<agemortsup;k++)
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+           }
+           else if(agev[m][i] >*agemax){
-     for (k=agegomp;k<agemortsup;k++){
+             *agemax=agev[m][i];
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-       sumlpop=sumlpop+lpop[k];
+           }
-     }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
-     tpop[agegomp]=sumlpop;
+         }
-     for (k=agegomp;k<(agemortsup-3);k++){
+         else { /* =9 */
-       /*  tpop[k+1]=2;*/
+           agev[m][i]=1;
-       tpop[k+1]=tpop[k]-lpop[k];
+           s[m][i]=-1;
-     }
+         }
+       }
+       else /*= 0 Unknown */
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+         agev[m][i]=1;
-     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]);
+   }
+   for (i=1; i<=imx; i++)  {
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     for(m=firstpass; (m<=lastpass); m++){
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+       if (s[m][i] > (nlstate+ndeath)) {
+         (*nberr)++;
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+         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);
-                      stepm, weightopt,\
+         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);
-                      model,imx,p,matcov,agemortsup);
+         return 1;
+       }
-     free_vector(lsurv,1,AGESUP);
+     }
-     free_vector(lpop,1,AGESUP);
+   }
-     free_vector(tpop,1,AGESUP);
-   } /* Endof if mle==-3 */
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
-   else{ /* For mle >=1 */
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
-     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");
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     globpr=1; /* to print the contributions */
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     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);
+   return (0);
-     for (k=1; k<=npar;k++)
+  /* endread:*/
-       printf(" %d %8.5f",k,p[k]);
+     printf("Exiting calandcheckages: ");
-     printf("\n");
+     return (1);
-     if(mle>=1){ /* Could be 1 or 2 */
+ }
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
+ #if defined(_MSC_VER)
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     /*--------- results files --------------*/
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     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);
+ //#include "stdafx.h"
+ //#include <stdio.h>
+ //#include <tchar.h>
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ //#include <windows.h>
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ //#include <iostream>
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
-     for(i=1,jk=1; i <=nlstate; i++){
-       for(k=1; k <=(nlstate+ndeath); k++){
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
-         if (k != i) {
-           printf("%d%d ",i,k);
+ BOOL IsWow64()
-           fprintf(ficlog,"%d%d ",i,k);
+ {
-           fprintf(ficres,"%1d%1d ",i,k);
+         BOOL bIsWow64 = FALSE;
-           for(j=1; j <=ncovmodel; j++){
-             printf("%lf ",p[jk]);
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
-             fprintf(ficlog,"%lf ",p[jk]);
+         //  (HANDLE, PBOOL);
-             fprintf(ficres,"%lf ",p[jk]);
-             jk++;
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
-           }
-           printf("\n");
+         HMODULE module = GetModuleHandle(_T("kernel32"));
-           fprintf(ficlog,"\n");
+         const char funcName[] = "IsWow64Process";
-           fprintf(ficres,"\n");
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
-         }
+                 GetProcAddress(module, funcName);
-       }
-     }
+         if (NULL != fnIsWow64Process)
-     if(mle!=0){
+         {
-       /* Computing hessian and covariance matrix */
+                 if (!fnIsWow64Process(GetCurrentProcess(),
-       ftolhess=ftol; /* Usually correct */
+                         &bIsWow64))
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+                         //throw std::exception("Unknown error");
-     }
+                         printf("Unknown error\n");
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+         }
-     printf("# Scales (for hessian or gradient estimation)\n");
+         return bIsWow64 != FALSE;
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ }
-     for(i=1,jk=1; i <=nlstate; i++){
+ #endif
-       for(j=1; j <=nlstate+ndeath; j++){
-         if (j!=i) {
+ void syscompilerinfo()
-           fprintf(ficres,"%1d%1d",i,j);
+  {
-           printf("%1d%1d",i,j);
+    /* #include "syscompilerinfo.h"*/
-           fprintf(ficlog,"%1d%1d",i,j);
+    /* command line Intel compiler 32bit windows, XP compatible:*/
-           for(k=1; k<=ncovmodel;k++){
+    /* /GS /W3 /Gy
-             printf(" %.5e",delti[jk]);
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
-             fprintf(ficlog," %.5e",delti[jk]);
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
-             fprintf(ficres," %.5e",delti[jk]);
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
-             jk++;
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
-           }
+       /* 64 bits */
-           printf("\n");
+    /*
-           fprintf(ficlog,"\n");
+      /GS /W3 /Gy
-           fprintf(ficres,"\n");
+      /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 */
-     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)
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
-       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");
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
-     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");
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
-     /* # 121 Var(a12)\n\ */
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+    */
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+    /* Link is $/ /* /OUT:"visual studio
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+       /PDB:"visual studio
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
-     /* Just to have a covariance matrix which will be more understandable
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
-        even is we still don't want to manage dictionary of variables
+       uiAccess='false'"
-     */
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
-     for(itimes=1;itimes<=2;itimes++){
+       /NOLOGO /TLBID:1
-       jj=0;
+    */
-       for(i=1; i <=nlstate; i++){
+ #if defined __INTEL_COMPILER
-         for(j=1; j <=nlstate+ndeath; j++){
+ #if defined(__GNUC__)
-           if(j==i) continue;
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
-           for(k=1; k<=ncovmodel;k++){
+ #endif
-             jj++;
+ #elif defined(__GNUC__)
-             ca[0]= k+'a'-1;ca[1]='\0';
+ #ifndef  __APPLE__
-             if(itimes==1){
+ #include <gnu/libc-version.h>  /* Only on gnu */
-               if(mle>=1)
+ #endif
-                 printf("#%1d%1d%d",i,j,k);
+    struct utsname sysInfo;
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+    int cross = CROSS;
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+    if (cross){
-             }else{
+            printf("Cross-");
-               if(mle>=1)
+            fprintf(ficlog, "Cross-");
-                 printf("%1d%1d%d",i,j,k);
+    }
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+ #endif
-               fprintf(ficres,"%1d%1d%d",i,j,k);
-             }
+ #include <stdint.h>
-             ll=0;
-             for(li=1;li <=nlstate; li++){
+    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+ #if defined(__clang__)
-                 if(lj==li) continue;
+    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
-                 for(lk=1;lk<=ncovmodel;lk++){
+ #endif
-                   ll++;
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
-                   if(ll<=jj){
+    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+ #endif
-                     if(ll<jj){
+ #if defined(__GNUC__) || defined(__GNUG__)
-                       if(itimes==1){
+    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
-                         if(mle>=1)
+ #endif
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ #if defined(__HP_cc) || defined(__HP_aCC)
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ #endif
-                       }else{
+ #if defined(__IBMC__) || defined(__IBMCPP__)
-                         if(mle>=1)
+    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
-                           printf(" %.5e",matcov[jj][ll]);
+ #endif
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+ #if defined(_MSC_VER)
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
-                       }
+ #endif
-                     }else{
+ #if defined(__PGI)
-                       if(itimes==1){
+    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
-                         if(mle>=1)
+ #endif
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+ #endif
-                       }else{
+    printf(" for ");fprintf(ficlog," for ");
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+     // Windows (x64 and x86)
-                       }
+    printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
-                     }
+ #elif __unix__ // all unices, not all compilers
-                   }
+     // Unix
-                 } /* end lk */
+    printf("Unix ");fprintf(ficlog,"Unix ");
-               } /* end lj */
+ #elif __linux__
-             } /* end li */
+     // linux
-             if(mle>=1)
+    printf("linux ");fprintf(ficlog,"linux ");
-               printf("\n");
+ #elif __APPLE__
-             fprintf(ficlog,"\n");
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
-             fprintf(ficres,"\n");
+    printf("Mac OS ");fprintf(ficlog,"Mac OS ");
-             numlinepar++;
+ #endif
-           } /* end k*/
-         } /*end j */
+ /*  __MINGW32__   */
-       } /* end i */
+ /*  __CYGWIN__   */
-     } /* end itimes */
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
-     fflush(ficlog);
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
-     fflush(ficres);
+ /* _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. */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ /* _M_X64 // Defined for compilations that target x64 processors. */
-       ungetc(c,ficpar);
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+ #if UINTPTR_MAX == 0xffffffff
-       fputs(line,ficparo);
+    printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
-     }
+ #elif UINTPTR_MAX == 0xffffffffffffffff
-     ungetc(c,ficpar);
+    printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
-     estepm=0;
+    printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ #endif
-     if (estepm==0 || estepm < stepm) estepm=stepm;
-     if (fage <= 2) {
+ #if defined(__GNUC__)
-       bage = ageminpar;
+ # if defined(__GNUC_PATCHLEVEL__)
-       fage = agemaxpar;
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     }
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+ # else
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+                             + __GNUC_MINOR__ * 100)
+ # endif
-     while((c=getc(ficpar))=='#' && c!= EOF){
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-       ungetc(c,ficpar);
+    fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+    if (uname(&sysInfo) != -1) {
-       fputs(line,ficparo);
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-     }
+      fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-     ungetc(c,ficpar);
+    }
+    else
-     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);
+       perror("uname() error");
-     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);
+    //#ifndef __INTEL_COMPILER
-     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);
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ #endif
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+    //   void main()
-       puts(line);
+    //   {
-       fputs(line,ficparo);
+ #if defined(_MSC_VER)
-     }
+    if (IsWow64()){
-     ungetc(c,ficpar);
+            printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+    else{
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+            printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+    }
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+    //      printf("\nPress Enter to continue...");
-     fprintf(ficres,"pop_based=%d\n",popbased);
+    //      getchar();
+    //   }
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+ #endif
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
-       fputs(line,ficparo);
+  }
-     }
-     ungetc(c,ficpar);
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-     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);
+   int i, j, k, i1 ;
-     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);
+   double ftolpl = 1.e-10;
-     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);
+   double age, agebase, agelim;
-     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);
+     strcpy(filerespl,"pl");
-     /* day and month of proj2 are not used but only year anproj2.*/
+     strcat(filerespl,fileres);
+     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;
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     }
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     pstamp(ficrespl);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     fprintf(ficrespl,"#Age ");
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+     fprintf(ficrespl,"\n");
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
-    /*------------ free_vector  -------------*/
-    /*  chdir(path); */
+     agebase=ageminpar;
+     agelim=agemaxpar;
-     free_ivector(wav,1,imx);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     i1=pow(2,cptcoveff);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     if (cptcovn < 1){i1=1;}
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     free_lvector(num,1,n);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     free_vector(agedc,1,n);
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+         k=k+1;
-     fclose(ficparo);
+         /* to clean */
-     fclose(ficres);
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
+         fprintf(ficrespl,"\n#******");
+         printf("\n#******");
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+         fprintf(ficlog,"\n#******");
+         for(j=1;j<=cptcoveff;j++) {
-     strcpy(filerespl,"pl");
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     strcat(filerespl,fileres);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+         }
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+         fprintf(ficrespl,"******\n");
-     }
+         printf("******\n");
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+         fprintf(ficlog,"******\n");
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     pstamp(ficrespl);
+         fprintf(ficrespl,"#Age ");
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+         for(j=1;j<=cptcoveff;j++) {
-     fprintf(ficrespl,"#Age ");
+           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+         }
-     fprintf(ficrespl,"\n");
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+         fprintf(ficrespl,"\n");
-     prlim=matrix(1,nlstate,1,nlstate);
+         for (age=agebase; age<=agelim; age++){
-     agebase=ageminpar;
+         /* for (age=agebase; age<=agebase; age++){ */
-     agelim=agemaxpar;
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-     ftolpl=1.e-10;
+           fprintf(ficrespl,"%.0f ",age );
-     i1=cptcoveff;
+           for(j=1;j<=cptcoveff;j++)
-     if (cptcovn < 1){i1=1;}
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           for(i=1; i<=nlstate;i++)
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+             fprintf(ficrespl," %.5f", prlim[i][i]);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+           fprintf(ficrespl,"\n");
-         k=k+1;
+         } /* Age */
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         /* was end of cptcod */
-         fprintf(ficrespl,"\n#******");
+     } /* cptcov */
-         printf("\n#******");
+         return 0;
-         fprintf(ficlog,"\n#******");
+ }
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ int hPijx(double *p, int bage, int fage){
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     /*------------- h Pij x at various ages ------------*/
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
+   int stepsize;
-         fprintf(ficrespl,"******\n");
+   int agelim;
-         printf("******\n");
+   int hstepm;
-         fprintf(ficlog,"******\n");
+   int nhstepm;
+   int h, i, i1, j, k;
-         for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   double agedeb;
-           fprintf(ficrespl,"%.0f ",age );
+   double ***p3mat;
-           for(j=1;j<=cptcoveff;j++)
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-           for(i=1; i<=nlstate;i++)
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
-           fprintf(ficrespl,"\n");
+       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);
-     fclose(ficrespl);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-     /*------------- h Pij x at various ages ------------*/
+     /*if (stepm<=24) stepsize=2;*/
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     agelim=AGESUP;
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     hstepm=stepsize*YEARM; /* Every year of age */
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
+     /* hstepm=1;   aff par mois*/
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     pstamp(ficrespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     i1= pow(2,cptcoveff);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     /*if (stepm<=24) stepsize=2;*/
+    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+    /*   k=k+1;  */
-     agelim=AGESUP;
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-     hstepm=stepsize*YEARM; /* Every year of age */
+       fprintf(ficrespij,"\n#****** ");
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     /* hstepm=1;   aff par mois*/
+       fprintf(ficrespij,"******\n");
-     pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         k=k+1;
-         fprintf(ficrespij,"\n#****** ");
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficrespij,"******\n");
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         for(i=1; i<=nlstate;i++)
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-           oldm=oldms;savm=savms;
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for(i=1; i<=nlstate;i++)
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+             for(j=1; j<=nlstate+ndeath;j++)
-           for(i=1; i<=nlstate;i++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespij,"\n");
-               fprintf(ficrespij," %1d-%1d",i,j);
+         }
-           fprintf(ficrespij,"\n");
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           for (h=0; h<=nhstepm; h++){
+         fprintf(ficrespij,"\n");
-             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]);
+         return 0;
-             fprintf(ficrespij,"\n");
+ }
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
+ /***********************************************/
-         }
+ /**************** Main Program *****************/
-       }
+ /***********************************************/
-     }
+ int main(int argc, char *argv[])
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+ {
+ #ifdef GSL
-     fclose(ficrespij);
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   int rval = GSL_CONTINUE;
-     for(i=1;i<=AGESUP;i++)
+   int status = GSL_SUCCESS;
-       for(j=1;j<=NCOVMAX;j++)
+   double ssval;
-         for(k=1;k<=NCOVMAX;k++)
+ #endif
-           probs[i][j][k]=0.;
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+   int jj, ll, li, lj, lk;
-     if(prevfcast==1){
+   int numlinepar=0; /* Current linenumber of parameter file */
-       /*    if(stepm ==1){*/
+   int itimes;
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+   int NDIM=2;
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+   int vpopbased=0;
-       /*      }  */
-       /*      else{ */
+   char ca[32], cb[32];
-       /*        erreur=108; */
+   /*  FILE *fichtm; *//* Html File */
-       /*        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); */
+   /* FILE *ficgp;*/ /*Gnuplot File */
-       /*        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); */
+   struct stat info;
-       /*      } */
+   double agedeb;
-     }
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double fret;
-     /*---------- Health expectancies and variances ------------*/
+   double dum; /* Dummy variable */
+   double ***p3mat;
-     strcpy(filerest,"t");
+   double ***mobaverage;
-     strcat(filerest,fileres);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+   char line[MAXLINE];
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   char pathr[MAXLINE], pathimach[MAXLINE];
-     }
+   char *tok, *val; /* pathtot */
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   int firstobs=1, lastobs=10;
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   int c,  h , cpt;
+   int jl;
+   int i1, j1, jk, stepsize;
-     strcpy(filerese,"e");
+   int *tab;
-     strcat(filerese,fileres);
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   int mobilav=0,popforecast=0;
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   int hstepm, nhstepm;
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   int agemortsup;
-     }
+   float  sumlpop=0.;
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-     strcpy(fileresstde,"stde");
+   double bage=0, fage=110, age, agelim, agebase;
-     strcat(fileresstde,fileres);
+   double ftolpl=FTOL;
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   double **prlim;
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   double ***param; /* Matrix of parameters */
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   double  *p;
-     }
+   double **matcov; /* Matrix of covariance */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   double ***delti3; /* Scale */
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
-     strcpy(filerescve,"cve");
+   double **varpl; /* Variances of prevalence limits by age */
-     strcat(filerescve,fileres);
+   double *epj, vepp;
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   double **ximort;
-     }
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   int *dcwave;
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   char z[1]="c";
-     strcpy(fileresv,"v");
-     strcat(fileresv,fileres);
+   /*char  *strt;*/
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   char strtend[80];
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-     }
+ /*   setlocale (LC_ALL, ""); */
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+ /*   setlocale (LC_MESSAGES, ""); */
-     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",\
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+   rstart_time = time(NULL);
-     */
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
-     if (mobilav!=0) {
+   curr_time=start_time;
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /*tml = *localtime(&start_time.tm_sec);*/
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   /* strcpy(strstart,asctime(&tml)); */
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   strcpy(strstart,asctime(&start_time));
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
+ /*  printf("Localtime (at start)=%s",strstart); */
-     }
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-         k=k+1;
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-         fprintf(ficrest,"\n#****** ");
+ /*   tp.tm_sec = mktime(&tmg); */
-         for(j=1;j<=cptcoveff;j++)
+ /*   strt=asctime(&tmg); */
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ /*   printf("Time(after) =%s",strstart);  */
-         fprintf(ficrest,"******\n");
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-         fprintf(ficreseij,"\n#****** ");
+ *  tm = *localtime(&time_value);
-         fprintf(ficresstdeij,"\n#****** ");
+ *  strstart=asctime(&tm);
-         fprintf(ficrescveij,"\n#****** ");
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-         for(j=1;j<=cptcoveff;j++) {
+ */
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   nberr=0; /* Number of errors and warnings */
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   nbwarn=0;
-         }
+ #ifdef WIN32
-         fprintf(ficreseij,"******\n");
+   _getcwd(pathcd, size);
-         fprintf(ficresstdeij,"******\n");
+ #else
-         fprintf(ficrescveij,"******\n");
+   getcwd(pathcd, size);
+ #endif
-         fprintf(ficresvij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+   printf("\n%s\n%s",version,fullversion);
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   if(argc <=1){
-         fprintf(ficresvij,"******\n");
+     printf("\nEnter the parameter file name: ");
+     fgets(pathr,FILENAMELENGTH,stdin);
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     i=strlen(pathr);
-         oldm=oldms;savm=savms;
+     if(pathr[i-1]=='\n')
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       pathr[i-1]='\0';
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+     i=strlen(pathr);
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       pathr[i-1]='\0';
-         oldm=oldms;savm=savms;
+    for (tok = pathr; tok != NULL; ){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+       printf("Pathr |%s|\n",pathr);
-         if(popbased==1){
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+       printf("val= |%s| pathr=%s\n",val,pathr);
-         }
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
-         pstamp(ficrest);
+     }
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+   }
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+   else{
-         fprintf(ficrest,"\n");
+     strcpy(pathtot,argv[1]);
+   }
-         epj=vector(1,nlstate+1);
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-         for(age=bage; age <=fage ;age++){
+   /*cygwin_split_path(pathtot,path,optionfile);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-           if (popbased==1) {
+   /* cutv(path,optionfile,pathtot,'\\');*/
-             if(mobilav ==0){
-               for(i=1; i<=nlstate;i++)
+   /* Split argv[0], imach program to get pathimach */
-                 prlim[i][i]=probs[(int)age][i][k];
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-             }else{ /* mobilav */
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-               for(i=1; i<=nlstate;i++)
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+  /*   strcpy(pathimach,argv[0]); */
-             }
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-           }
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           fprintf(ficrest," %4.0f",age);
+ #ifdef WIN32
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+   _chdir(path); /* Can be a relative path */
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+ #else
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+   chdir(path); /* Can be a relative path */
-             }
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
-             epj[nlstate+1] +=epj[j];
+ #endif
-           }
+   printf("Current directory %s!\n",pathcd);
+   strcpy(command,"mkdir ");
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   strcat(command,optionfilefiname);
-             for(j=1;j <=nlstate;j++)
+   if((outcmd=system(command)) != 0){
-               vepp += vareij[i][j][(int)age];
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-           for(j=1;j <=nlstate;j++){
+     /* fclose(ficlog); */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ /*     exit(1); */
-           }
+   }
-           fprintf(ficrest,"\n");
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-         }
+ /*     perror("mkdir"); */
-         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);
+   /*-------- arguments in the command line --------*/
-       }
-     }
+   /* Log file */
-     free_vector(weight,1,n);
+   strcat(filelog, optionfilefiname);
-     free_imatrix(Tvard,1,15,1,2);
+   strcat(filelog,".log");    /* */
-     free_imatrix(s,1,maxwav+1,1,n);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-     free_matrix(anint,1,maxwav,1,n);
+     printf("Problem with logfile %s\n",filelog);
-     free_matrix(mint,1,maxwav,1,n);
+     goto end;
-     free_ivector(cod,1,n);
+   }
-     free_ivector(tab,1,NCOVMAX);
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     fclose(ficreseij);
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-     fclose(ficresstdeij);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-     fclose(ficrescveij);
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     fclose(ficresvij);
+  path=%s \n\
-     fclose(ficrest);
+  optionfile=%s\n\
-     fclose(ficpar);
+  optionfilext=%s\n\
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     /*------- Variance of period (stable) prevalence------*/
+   syscompilerinfo();
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
+   printf("Local time (at start):%s",strstart);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+   fflush(ficlog);
-       exit(0);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     }
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+   /* */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   strcpy(fileres,"r");
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   strcat(fileres, optionfilefiname);
-         k=k+1;
+   strcat(fileres,".txt");    /* Other files have txt extension */
-         fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+   /*---------arguments file --------*/
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-         oldm=oldms;savm=savms;
+     fflush(ficlog);
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     /* goto end; */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     exit(70);
-       }
+   }
-     }
-     fclose(ficresvpl);
+   strcpy(filereso,"o");
-     /*---------- End : free ----------------*/
+   strcat(filereso,fileres);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-   }  /* mle==-3 arrives here for freeing */
+     fflush(ficlog);
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     goto end;
-     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);
+   /* Reads comments: lines beginning with '#' */
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   numlinepar=0;
-     free_matrix(covar,0,NCOVMAX,1,n);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     free_matrix(matcov,1,npar,1,npar);
+     ungetc(c,ficpar);
-     /*free_vector(delti,1,npar);*/
+     fgets(line, MAXLINE, ficpar);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     numlinepar++;
-     free_matrix(agev,1,maxwav,1,imx);
+     fputs(line,stdout);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
-     free_ivector(ncodemax,1,8);
+   }
-     free_ivector(Tvar,1,15);
+   ungetc(c,ficpar);
-     free_ivector(Tprod,1,15);
-     free_ivector(Tvaraff,1,15);
+   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);
-     free_ivector(Tage,1,15);
+   numlinepar++;
-     free_ivector(Tcode,1,100);
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   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);
-     free_imatrix(codtab,1,100,1,10);
+   fflush(ficlog);
-   fflush(fichtm);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-   fflush(ficgp);
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
-   if((nberr >0) || (nbwarn>0)){
+     fputs(line, stdout);
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     //puts(line);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     fputs(line,ficparo);
-   }else{
+     fputs(line,ficlog);
-     printf("End of Imach\n");
+   }
-     fprintf(ficlog,"End of Imach\n");
+   ungetc(c,ficpar);
-   }
-   printf("See log file on %s\n",filelog);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-   (void) gettimeofday(&end_time,&tzp);
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-   tm = *localtime(&end_time.tv_sec);
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-   tmg = *gmtime(&end_time.tv_sec);
+      v1+v2*age+v2*v3 makes cptcovn = 3
-   strcpy(strtend,asctime(&tm));
+   */
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   if (strlen(model)>1)
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     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*/
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   else
+     ncovmodel=2;
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     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(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     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);
-   fclose(fichtm);
+     fflush(stdout);
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     fclose (ficlog);
-   fclose(fichtmcov);
+     goto end;
-   fclose(ficgp);
+   }
-   fclose(ficlog);
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   /*------ End -----------*/
+   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 */
-    printf("Before Current directory %s!\n",pathcd);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-    if(chdir(pathcd) != 0)
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     printf("Can't move to directory %s!\n",path);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-   if(getcwd(pathcd,MAXLINE) > 0)
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     printf("Current directory %s!\n",pathcd);
+     fclose (ficparo);
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     fclose (ficlog);
-   sprintf(plotcmd,"gnuplot");
+     goto end;
- #ifndef UNIX
+     exit(0);
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+   }
- #endif
+   else if(mle==-3) {
-   if(!stat(plotcmd,&info)){
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     }else
+     matcov=matrix(1,npar,1,npar);
-       strcpy(pplotcmd,plotcmd);
+   }
- #ifdef UNIX
+   else{
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     /* Read guessed parameters */
-     if(!stat(plotcmd,&info)){
+     /* Reads comments: lines beginning with '#' */
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     }else
+       ungetc(c,ficpar);
-       strcpy(pplotcmd,plotcmd);
+       fgets(line, MAXLINE, ficpar);
- #endif
+       numlinepar++;
-   }else
+       fputs(line,stdout);
-     strcpy(pplotcmd,plotcmd);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     }
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     ungetc(c,ficpar);
-   if((outcmd=system(plotcmd)) != 0){
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     printf("\n Problem with gnuplot\n");
+     for(i=1; i <=nlstate; i++){
-   }
+       j=0;
-   printf(" Wait...");
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-   while (z[0] != 'q') {
+         if(jj==i) continue;
-     /* chdir(path); */
+         j++;
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     scanf("%s",z);
+         if ((i1 != i) && (j1 != j)){
- /*     if (z[0] == 'c') system("./imach"); */
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-     if (z[0] == 'e') {
+ It might be a problem of design; if ncovcol and the model are correct\n \
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-       system(optionfilehtm);
+           exit(1);
-     }
+         }
-     else if (z[0] == 'g') system(plotcmd);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     else if (z[0] == 'q') exit(0);
+         if(mle==1)
-   }
+           printf("%1d%1d",i,j);
-   end:
+         fprintf(ficlog,"%1d%1d",i,j);
-   while (z[0] != 'q') {
+         for(k=1; k<=ncovmodel;k++){
-     printf("\nType  q for exiting: ");
+           fscanf(ficpar," %lf",&param[i][j][k]);
-     scanf("%s",z);
+           if(mle==1){
-   }
+             printf(" %lf",param[i][j][k]);
- }
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads scales values */
+     p=param[1][1];
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ( (i1-i) * (j1-j) != 0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
+       }
+     }
+     fflush(ficlog);
+     /* Reads covariance matrix */
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
+       if(mle==1)
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
+       fprintf(ficparo,"%s",str);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
+         }
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
+       fscanf(ficpar,"\n");
+       numlinepar++;
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
+     }
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
+   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 */
+   /* 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
+                       */
+   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 > 2)
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
+   h=0;
+   /*if (cptcovn > 0) */
+   m=pow(2,cptcoveff);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
+           h++;
+           if (h>m)
+             h=1;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     h     1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     1
+            */
+           codtab[h][k]=j;
+           /*codtab[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);
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+ #ifdef WIN32
+   _chdir(optionfilefiname); /* Move to directory named optionfile */
+ #else
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+ #endif
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     /*printf("%lf %lf", p[1], p[2]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #else
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #else
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%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("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     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(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
+     prlim=matrix(1,nlstate,1,nlstate);
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar);
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           oldm=oldms;savm=savms; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f",age);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+ #ifdef WIN32
+    if (_chdir(pathcd) != 0)
+            printf("Can't move to directory %s!\n",path);
+    if(_getcwd(pathcd,MAXLINE) > 0)
+ #else
+    if(chdir(pathcd) != 0)
+            printf("Can't move to directory %s!\n", path);
+    if (getcwd(pathcd, MAXLINE) > 0)
+ #endif
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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