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Diff for /imach/src/imach.c between versions 1.125 and 1.177

-version 1.125, 2006/04/04 15:20:31
+version 1.177, 2015/01/03 18:40:56
  Line 1
  /* $Id$
    $State$
    $Log$
+   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;
+ #include <math.h>
- /* #include <sys/time.h> */
+ #include <stdio.h>
- #include <time.h>
+ #include <stdlib.h>
- #include "timeval.h"
+ #include <string.h>
- /* #include <libintl.h> */
+ #ifdef _WIN32
- /* #define _(String) gettext (String) */
+ #include <io.h>
+ #include <windows.h>
- #define MAXLINE 256
+ #include <tchar.h>
+ #else
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <unistd.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #endif
- #define FILENAMELENGTH 132
+ #include <limits.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #include <sys/types.h>
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #if defined(__GNUC__)
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #include <sys/utsname.h> /* Doesn't work on Windows */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #endif
- #define NINTERVMAX 8
+ #include <sys/stat.h>
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #include <errno.h>
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ /* extern int errno; */
- #define NCOVMAX 8 /* Maximum number of covariates */
- #define MAXN 20000
+ /* #ifdef LINUX */
- #define YEARM 12. /* Number of months per year */
+ /* #include <time.h> */
- #define AGESUP 130
+ /* #include "timeval.h" */
- #define AGEBASE 40
+ /* #else */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ /* #include <sys/time.h> */
- #ifdef UNIX
+ /* #endif */
- #define DIRSEPARATOR '/'
- #define CHARSEPARATOR "/"
+ #include <time.h>
- #define ODIRSEPARATOR '\\'
- #else
+ #ifdef GSL
- #define DIRSEPARATOR '\\'
+ #include <gsl/gsl_errno.h>
- #define CHARSEPARATOR "\\"
+ #include <gsl/gsl_multimin.h>
- #define ODIRSEPARATOR '/'
+ #endif
- #endif
- /* $Id$ */
+ #ifdef NLOPT
- /* $State$ */
+ #include <nlopt.h>
+ typedef struct {
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+   double (* function)(double [] );
- char fullversion[]="$Revision$ $Date$";
+ } myfunc_data ;
- char strstart[80];
+ #endif
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ /* #include <libintl.h> */
- int nvar;
+ /* #define _(String) gettext (String) */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
- int npar=NPARMAX;
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int nlstate=2; /* Number of live states */
- int ndeath=1; /* Number of dead states */
+ #define GNUPLOTPROGRAM "gnuplot"
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int popbased=0;
+ #define FILENAMELENGTH 132
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int maxwav; /* Maxim number of waves */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int jmin, jmax; /* min, max spacing between 2 waves */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
-                    to the likelihood and the sum of weights (done by funcone)*/
- int mle, weightopt;
+ #define NINTERVMAX 8
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- double jmean; /* Mean space between 2 waves */
+ #define MAXN 20000
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define YEARM 12. /**< Number of months per year */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define AGESUP 130
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define AGEBASE 40
- FILE *ficlog, *ficrespow;
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- int globpr; /* Global variable for printing or not */
+ #ifdef _WIN32
- double fretone; /* Only one call to likelihood */
+ #define DIRSEPARATOR '\\'
- long ipmx; /* Number of contributions */
+ #define CHARSEPARATOR "\\"
- double sw; /* Sum of weights */
+ #define ODIRSEPARATOR '/'
- char filerespow[FILENAMELENGTH];
+ #else
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #define DIRSEPARATOR '/'
- FILE *ficresilk;
+ #define CHARSEPARATOR "/"
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define ODIRSEPARATOR '\\'
- FILE *ficresprobmorprev;
+ #endif
- FILE *fichtm, *fichtmcov; /* Html File */
- FILE *ficreseij;
+ /* $Id$ */
- char filerese[FILENAMELENGTH];
+ /* $State$ */
- FILE *ficresstdeij;
- char fileresstde[FILENAMELENGTH];
+ char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- FILE *ficrescveij;
+ char fullversion[]="$Revision$ $Date$";
- char filerescve[FILENAMELENGTH];
+ char strstart[80];
- FILE  *ficresvij;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- char fileresv[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- FILE  *ficresvpl;
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char fileresvpl[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- char title[MAXLINE];
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- char command[FILENAMELENGTH];
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- int  outcmd=0;
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int cptcov=0; /* Working variable */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int npar=NPARMAX;
+ int nlstate=2; /* Number of live states */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int ndeath=1; /* Number of dead states */
- char filerest[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char fileregp[FILENAMELENGTH];
+ int popbased=0;
- char popfile[FILENAMELENGTH];
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int maxwav=0; /* Maxim number of waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- struct timezone tzp;
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- extern int gettimeofday();
+                    to the likelihood and the sum of weights (done by funcone)*/
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int mle=1, weightopt=0;
- long time_value;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- extern long time();
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- char strcurr[80], strfor[80];
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- char *endptr;
+ int countcallfunc=0;  /* Count the number of calls to func */
- long lval;
+ double jmean=1; /* Mean space between 2 waves */
- double dval;
+ double **matprod2(); /* test */
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define NR_END 1
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- #define FREE_ARG char*
+ /*FILE *fic ; */ /* Used in readdata only */
- #define FTOL 1.0e-10
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficlog, *ficrespow;
- #define NRANSI
+ int globpr=0; /* Global variable for printing or not */
- #define ITMAX 200
+ double fretone; /* Only one call to likelihood */
+ long ipmx=0; /* Number of contributions */
- #define TOL 2.0e-4
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
- #define CGOLD 0.3819660
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- #define ZEPS 1.0e-10
+ FILE *ficresilk;
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficresprobmorprev;
- #define GOLD 1.618034
+ FILE *fichtm, *fichtmcov; /* Html File */
- #define GLIMIT 100.0
+ FILE *ficreseij;
- #define TINY 1.0e-20
+ char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
- static double maxarg1,maxarg2;
+ char fileresstde[FILENAMELENGTH];
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ FILE *ficrescveij;
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char filerescve[FILENAMELENGTH];
+ FILE  *ficresvij;
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char fileresv[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- static double sqrarg;
+ char title[MAXLINE];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- int imx;
+ int  outcmd=0;
- int stepm=1;
- /* Stepm, step in month: minimum step interpolation*/
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- int estepm;
+ char filelog[FILENAMELENGTH]; /* Log file */
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
- int m,nb;
+ char popfile[FILENAMELENGTH];
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- double *ageexmed,*agecens;
+ /* struct timezone tzp; */
- double dateintmean=0;
+ /* extern int gettimeofday(); */
+ struct tm tml, *gmtime(), *localtime();
- double *weight;
- int **s; /* Status */
+ extern time_t time();
- double *agedc, **covar, idx;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- double *lsurv, *lpop, *tpop;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
+ struct tm tm;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ char strcurr[80], strfor[80];
- /**************** split *************************/
+ char *endptr;
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ long lval;
- {
+ double dval;
-   /* 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)
+ #define NR_END 1
-   */
+ #define FREE_ARG char*
-   char  *ss;                            /* pointer */
+ #define FTOL 1.0e-10
-   int   l1, l2;                         /* length counters */
+ #define NRANSI
-   l1 = strlen(path );                   /* length of path */
+ #define ITMAX 200
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define TOL 2.0e-4
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ #define CGOLD 0.3819660
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ #define ZEPS 1.0e-10
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     /* get current working directory */
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define GOLD 1.618034
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define GLIMIT 100.0
-       return( GLOCK_ERROR_GETCWD );
+ #define TINY 1.0e-20
-     }
-     /* got dirc from getcwd*/
+ static double maxarg1,maxarg2;
-     printf(" DIRC = %s \n",dirc);
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-   } else {                              /* strip direcotry from path */
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     ss++;                               /* after this, the filename */
-     l2 = strlen( ss );                  /* length of filename */
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define rint(a) floor(a+0.5)
-     strcpy( name, ss );         /* save file name */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ /* #define mytinydouble 1.0e-16 */
-     dirc[l1-l2] = 0;                    /* add zero */
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     printf(" DIRC2 = %s \n",dirc);
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-   }
+ /* static double dsqrarg; */
-   /* We add a separator at the end of dirc if not exists */
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-   l1 = strlen( dirc );                  /* length of directory */
+ static double sqrarg;
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-     dirc[l1] =  DIRSEPARATOR;
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     dirc[l1+1] = 0;
+ int agegomp= AGEGOMP;
-     printf(" DIRC3 = %s \n",dirc);
-   }
+ int imx;
-   ss = strrchr( name, '.' );            /* find last / */
+ int stepm=1;
-   if (ss >0){
+ /* Stepm, step in month: minimum step interpolation*/
-     ss++;
-     strcpy(ext,ss);                     /* save extension */
+ int estepm;
-     l1= strlen( name);
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     l2= strlen(ss)+1;
-     strncpy( finame, name, l1-l2);
+ int m,nb;
-     finame[l1-l2]= 0;
+ long *num;
-   }
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-   return( 0 );                          /* we're done */
+ double **pmmij, ***probs;
- }
+ double *ageexmed,*agecens;
+ double dateintmean=0;
- /******************************************/
+ double *weight;
+ int **s; /* Status */
- void replace_back_to_slash(char *s, char*t)
+ double *agedc;
- {
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   int i;
+                   * covar=matrix(0,NCOVMAX,1,n);
-   int lg=0;
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   i=0;
+ double  idx;
-   lg=strlen(t);
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-   for(i=0; i<= lg; i++) {
+ int *Ndum; /** Freq of modality (tricode */
-     (s[i] = t[i]);
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-     if (t[i]== '\\') s[i]='/';
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   }
+ double *lsurv, *lpop, *tpop;
- }
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- int nbocc(char *s, char occ)
+ double ftolhess; /**< Tolerance for computing hessian */
- {
-   int i,j=0;
+ /**************** split *************************/
-   int lg=20;
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   i=0;
+ {
-   lg=strlen(s);
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   for(i=0; i<= lg; i++) {
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   if  (s[i] == occ ) j++;
+   */
-   }
+   char  *ss;                            /* pointer */
-   return j;
+   int   l1, l2;                         /* length counters */
- }
+   l1 = strlen(path );                   /* length of path */
- void cutv(char *u,char *v, char*t, char occ)
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- {
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+     strcpy( name, path );               /* we got the fullname name because no directory */
-      gives u="abcedf" and v="ghi2j" */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   int i,lg,j,p=0;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   i=0;
+     /* get current working directory */
-   for(j=0; j<=strlen(t)-1; j++) {
+     /*    extern  char* getcwd ( char *buf , int len);*/
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   }
+       return( GLOCK_ERROR_GETCWD );
+     }
-   lg=strlen(t);
+     /* got dirc from getcwd*/
-   for(j=0; j<p; j++) {
+     printf(" DIRC = %s \n",dirc);
-     (u[j] = t[j]);
+   } else {                              /* strip direcotry from path */
-   }
+     ss++;                               /* after this, the filename */
-      u[p]='\0';
+     l2 = strlen( ss );                  /* length of filename */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-    for(j=0; j<= lg; j++) {
+     strcpy( name, ss );         /* save file name */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   }
+     dirc[l1-l2] = 0;                    /* add zero */
- }
+     printf(" DIRC2 = %s \n",dirc);
+   }
- /********************** nrerror ********************/
+   /* We add a separator at the end of dirc if not exists */
+   l1 = strlen( dirc );                  /* length of directory */
- void nrerror(char error_text[])
+   if( dirc[l1-1] != DIRSEPARATOR ){
- {
+     dirc[l1] =  DIRSEPARATOR;
-   fprintf(stderr,"ERREUR ...\n");
+     dirc[l1+1] = 0;
-   fprintf(stderr,"%s\n",error_text);
+     printf(" DIRC3 = %s \n",dirc);
-   exit(EXIT_FAILURE);
+   }
- }
+   ss = strrchr( name, '.' );            /* find last / */
- /*********************** vector *******************/
+   if (ss >0){
- double *vector(int nl, int nh)
+     ss++;
- {
+     strcpy(ext,ss);                     /* save extension */
-   double *v;
+     l1= strlen( name);
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     l2= strlen(ss)+1;
-   if (!v) nrerror("allocation failure in vector");
+     strncpy( finame, name, l1-l2);
-   return v-nl+NR_END;
+     finame[l1-l2]= 0;
- }
+   }
- /************************ free vector ******************/
+   return( 0 );                          /* we're done */
- void free_vector(double*v, int nl, int nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ /******************************************/
- /************************ivector *******************************/
+ void replace_back_to_slash(char *s, char*t)
- int *ivector(long nl,long nh)
+ {
- {
+   int i;
-   int *v;
+   int lg=0;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   i=0;
-   if (!v) nrerror("allocation failure in ivector");
+   lg=strlen(t);
-   return v-nl+NR_END;
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- /******************free ivector **************************/
+   }
- void free_ivector(int *v, long nl, long nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
+ char *trimbb(char *out, char *in)
- }
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+   char *s;
- /************************lvector *******************************/
+   s=out;
- long *lvector(long nl,long nh)
+   while (*in != '\0'){
- {
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-   long *v;
+       in++;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+     }
-   if (!v) nrerror("allocation failure in ivector");
+     *out++ = *in++;
-   return v-nl+NR_END;
+   }
- }
+   *out='\0';
+   return s;
- /******************free lvector **************************/
+ }
- void free_lvector(long *v, long nl, long nh)
- {
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-   free((FREE_ARG)(v+nl-NR_END));
+ {
- }
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- /******************* imatrix *******************************/
+      gives blocc="abcdef2ghi" and alocc="j".
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   */
- {
+   char *s, *t;
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   t=in;s=in;
-   int **m;
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
-   /* allocate pointers to rows */
+   }
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   if( *in == occ){
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     *(alocc)='\0';
-   m += NR_END;
+     s=++in;
-   m -= nrl;
+   }
+   if (s == t) {/* occ not found */
-   /* allocate rows and set pointers to them */
+     *(alocc-(in-s))='\0';
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+     in=s;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   }
-   m[nrl] += NR_END;
+   while ( *in != '\0'){
-   m[nrl] -= ncl;
+     *blocc++ = *in++;
+   }
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   *blocc='\0';
-   /* return pointer to array of pointers to rows */
+   return t;
-   return m;
+ }
- }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
- /****************** free_imatrix *************************/
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
- void free_imatrix(m,nrl,nrh,ncl,nch)
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-       int **m;
+      gives blocc="abcdef2ghi" and alocc="j".
-       long nch,ncl,nrh,nrl;
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-      /* free an int matrix allocated by imatrix() */
+   */
- {
+   char *s, *t;
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   t=in;s=in;
-   free((FREE_ARG) (m+nrl-NR_END));
+   while (*in != '\0'){
- }
+     while( *in == occ){
+       *blocc++ = *in++;
- /******************* matrix *******************************/
+       s=in;
- double **matrix(long nrl, long nrh, long ncl, long nch)
+     }
- {
+     *blocc++ = *in++;
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   }
-   double **m;
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   else
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     *(blocc-(in-s)-1)='\0';
-   m += NR_END;
+   in=s;
-   m -= nrl;
+   while ( *in != '\0'){
+     *alocc++ = *in++;
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+   *alocc='\0';
-   m[nrl] -= ncl;
+   return s;
+ }
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   return m;
+ int nbocc(char *s, char occ)
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ {
-    */
+   int i,j=0;
- }
+   int lg=20;
+   i=0;
- /*************************free matrix ************************/
+   lg=strlen(s);
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   for(i=0; i<= lg; i++) {
- {
+   if  (s[i] == occ ) j++;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   }
-   free((FREE_ARG)(m+nrl-NR_END));
+   return j;
  }
- /******************* ma3x *******************************/
+ /* void cutv(char *u,char *v, char*t, char occ) */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /* { */
- {
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   double ***m;
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
+ /*   int i,lg,j,p=0; */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*   i=0; */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*   lg=strlen(t); */
-   m += NR_END;
+ /*   for(j=0; j<=lg-1; j++) { */
-   m -= nrl;
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   for(j=0; j<p; j++) { */
-   m[nrl] += NR_END;
+ /*     (u[j] = t[j]); */
-   m[nrl] -= ncl;
+ /*   } */
+ /*      u[p]='\0'; */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*    for(j=0; j<= lg; j++) { */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ /*   } */
-   m[nrl][ncl] += NR_END;
+ /* } */
-   m[nrl][ncl] -= nll;
-   for (j=ncl+1; j<=nch; j++)
+ #ifdef _WIN32
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ char * strsep(char **pp, const char *delim)
+ {
-   for (i=nrl+1; i<=nrh; i++) {
+   char *p, *q;
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-     for (j=ncl+1; j<=nch; j++)
+   if ((p = *pp) == NULL)
-       m[i][j]=m[i][j-1]+nlay;
+     return 0;
-   }
+   if ((q = strpbrk (p, delim)) != NULL)
-   return m;
+   {
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+     *pp = q + 1;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+     *q = '\0';
-   */
+   }
- }
+   else
+     *pp = 0;
- /*************************free ma3x ************************/
+   return p;
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ }
- {
+ #endif
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ /********************** nrerror ********************/
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ void nrerror(char error_text[])
+ {
- /*************** function subdirf ***********/
+   fprintf(stderr,"ERREUR ...\n");
- char *subdirf(char fileres[])
+   fprintf(stderr,"%s\n",error_text);
- {
+   exit(EXIT_FAILURE);
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
+ /*********************** vector *******************/
-   strcat(tmpout,"/"); /* Add to the right */
+ double *vector(int nl, int nh)
-   strcat(tmpout,fileres);
+ {
-   return tmpout;
+   double *v;
- }
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   if (!v) nrerror("allocation failure in vector");
- /*************** function subdirf2 ***********/
+   return v-nl+NR_END;
- char *subdirf2(char fileres[], char *preop)
+ }
- {
+ /************************ free vector ******************/
-   /* Caution optionfilefiname is hidden */
+ void free_vector(double*v, int nl, int nh)
-   strcpy(tmpout,optionfilefiname);
+ {
-   strcat(tmpout,"/");
+   free((FREE_ARG)(v+nl-NR_END));
-   strcat(tmpout,preop);
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /************************ivector *******************************/
- }
+ int *ivector(long nl,long nh)
+ {
- /*************** function subdirf3 ***********/
+   int *v;
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- {
+   if (!v) nrerror("allocation failure in ivector");
+   return v-nl+NR_END;
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+ /******************free ivector **************************/
-   strcat(tmpout,preop);
+ void free_ivector(int *v, long nl, long nh)
-   strcat(tmpout,preop2);
+ {
-   strcat(tmpout,fileres);
+   free((FREE_ARG)(v+nl-NR_END));
-   return tmpout;
+ }
- }
+ /************************lvector *******************************/
- /***************** f1dim *************************/
+ long *lvector(long nl,long nh)
- extern int ncom;
+ {
- extern double *pcom,*xicom;
+   long *v;
- extern double (*nrfunc)(double []);
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   if (!v) nrerror("allocation failure in ivector");
- double f1dim(double x)
+   return v-nl+NR_END;
- {
+ }
-   int j;
-   double f;
+ /******************free lvector **************************/
-   double *xt;
+ void free_lvector(long *v, long nl, long nh)
+ {
-   xt=vector(1,ncom);
+   free((FREE_ARG)(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);
+ /******************* imatrix *******************************/
-   return f;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
- }
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ {
- /*****************brent *************************/
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   int **m;
- {
-   int iter;
+   /* allocate pointers to rows */
-   double a,b,d,etemp;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   double fu,fv,fw,fx;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   double ftemp;
+   m += NR_END;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   m -= nrl;
-   double e=0.0;
-   a=(ax < cx ? ax : cx);
+   /* allocate rows and set pointers to them */
-   b=(ax > cx ? ax : cx);
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   x=w=v=bx;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   fw=fv=fx=(*f)(x);
+   m[nrl] += NR_END;
-   for (iter=1;iter<=ITMAX;iter++) {
+   m[nrl] -= ncl;
-     xm=0.5*(a+b);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     printf(".");fflush(stdout);
+   /* return pointer to array of pointers to rows */
-     fprintf(ficlog,".");fflush(ficlog);
+   return m;
- #ifdef DEBUG
+ }
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ /****************** free_imatrix *************************/
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+ void free_imatrix(m,nrl,nrh,ncl,nch)
- #endif
+       int **m;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+       long nch,ncl,nrh,nrl;
-       *xmin=x;
+      /* free an int matrix allocated by imatrix() */
-       return fx;
+ {
-     }
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     ftemp=fu;
+   free((FREE_ARG) (m+nrl-NR_END));
-     if (fabs(e) > tol1) {
+ }
-       r=(x-w)*(fx-fv);
-       q=(x-v)*(fx-fw);
+ /******************* matrix *******************************/
-       p=(x-v)*q-(x-w)*r;
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       q=2.0*(q-r);
+ {
-       if (q > 0.0) p = -p;
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-       q=fabs(q);
+   double **m;
-       etemp=e;
-       e=d;
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   if (!m) nrerror("allocation failure 1 in matrix()");
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   m += NR_END;
-       else {
+   m -= nrl;
-         d=p/q;
-         u=x+d;
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-         if (u-a < tol2 || b-u < tol2)
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-           d=SIGN(tol1,xm-x);
+   m[nrl] += NR_END;
-       }
+   m[nrl] -= ncl;
-     } else {
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     }
+   return m;
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-     fu=(*f)(u);
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-     if (fu <= fx) {
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-       if (u >= x) a=x; else b=x;
+    */
-       SHFT(v,w,x,u)
+ }
-         SHFT(fv,fw,fx,fu)
-         } else {
+ /*************************free matrix ************************/
-           if (u < x) a=u; else b=u;
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-           if (fu <= fw || w == x) {
+ {
-             v=w;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-             w=u;
+   free((FREE_ARG)(m+nrl-NR_END));
-             fv=fw;
+ }
-             fw=fu;
-           } else if (fu <= fv || v == x || v == w) {
+ /******************* ma3x *******************************/
-             v=u;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-             fv=fu;
+ {
-           }
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-         }
+   double ***m;
-   }
-   nrerror("Too many iterations in brent");
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   *xmin=x;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   return fx;
+   m += NR_END;
- }
+   m -= nrl;
- /****************** mnbrak ***********************/
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   m[nrl] += NR_END;
-             double (*func)(double))
+   m[nrl] -= ncl;
- {
-   double ulim,u,r,q, dum;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   double fu;
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   *fa=(*func)(*ax);
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   *fb=(*func)(*bx);
+   m[nrl][ncl] += NR_END;
-   if (*fb > *fa) {
+   m[nrl][ncl] -= nll;
-     SHFT(dum,*ax,*bx,dum)
+   for (j=ncl+1; j<=nch; j++)
-       SHFT(dum,*fb,*fa,dum)
+     m[nrl][j]=m[nrl][j-1]+nlay;
-       }
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   for (i=nrl+1; i<=nrh; i++) {
-   *fc=(*func)(*cx);
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   while (*fb > *fc) {
+     for (j=ncl+1; j<=nch; j++)
-     r=(*bx-*ax)*(*fb-*fc);
+       m[i][j]=m[i][j-1]+nlay;
-     q=(*bx-*cx)*(*fb-*fa);
+   }
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   return m;
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   */
-       fu=(*func)(u);
+ }
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       fu=(*func)(u);
+ /*************************free ma3x ************************/
-       if (fu < *fc) {
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ {
-           SHFT(*fb,*fc,fu,(*func)(u))
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-           }
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   free((FREE_ARG)(m+nrl-NR_END));
-       u=ulim;
+ }
-       fu=(*func)(u);
-     } else {
+ /*************** function subdirf ***********/
-       u=(*cx)+GOLD*(*cx-*bx);
+ char *subdirf(char fileres[])
-       fu=(*func)(u);
+ {
-     }
+   /* Caution optionfilefiname is hidden */
-     SHFT(*ax,*bx,*cx,u)
+   strcpy(tmpout,optionfilefiname);
-       SHFT(*fa,*fb,*fc,fu)
+   strcat(tmpout,"/"); /* Add to the right */
-       }
+   strcat(tmpout,fileres);
- }
+   return tmpout;
+ }
- /*************** linmin ************************/
+ /*************** function subdirf2 ***********/
- int ncom;
+ char *subdirf2(char fileres[], char *preop)
- double *pcom,*xicom;
+ {
- double (*nrfunc)(double []);
+   /* Caution optionfilefiname is hidden */
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   strcpy(tmpout,optionfilefiname);
- {
+   strcat(tmpout,"/");
-   double brent(double ax, double bx, double cx,
+   strcat(tmpout,preop);
-                double (*f)(double), double tol, double *xmin);
+   strcat(tmpout,fileres);
-   double f1dim(double x);
+   return tmpout;
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ }
-               double *fc, double (*func)(double));
-   int j;
+ /*************** function subdirf3 ***********/
-   double xx,xmin,bx,ax;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   double fx,fb,fa;
+ {
-   ncom=n;
+   /* Caution optionfilefiname is hidden */
-   pcom=vector(1,n);
+   strcpy(tmpout,optionfilefiname);
-   xicom=vector(1,n);
+   strcat(tmpout,"/");
-   nrfunc=func;
+   strcat(tmpout,preop);
-   for (j=1;j<=n;j++) {
+   strcat(tmpout,preop2);
-     pcom[j]=p[j];
+   strcat(tmpout,fileres);
-     xicom[j]=xi[j];
+   return tmpout;
-   }
+ }
-   ax=0.0;
-   xx=1.0;
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ {
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   long sec_left, days, hours, minutes;
- #ifdef DEBUG
+   days = (time_sec) / (60*60*24);
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   sec_left = (time_sec) % (60*60*24);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   hours = (sec_left) / (60*60) ;
- #endif
+   sec_left = (sec_left) %(60*60);
-   for (j=1;j<=n;j++) {
+   minutes = (sec_left) /60;
-     xi[j] *= xmin;
+   sec_left = (sec_left) % (60);
-     p[j] += xi[j];
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-   }
+   return ascdiff;
-   free_vector(xicom,1,n);
+ }
-   free_vector(pcom,1,n);
- }
+ /***************** f1dim *************************/
+ extern int ncom;
- char *asc_diff_time(long time_sec, char ascdiff[])
+ extern double *pcom,*xicom;
- {
+ extern double (*nrfunc)(double []);
-   long sec_left, days, hours, minutes;
-   days = (time_sec) / (60*60*24);
+ double f1dim(double x)
-   sec_left = (time_sec) % (60*60*24);
+ {
-   hours = (sec_left) / (60*60) ;
+   int j;
-   sec_left = (sec_left) %(60*60);
+   double f;
-   minutes = (sec_left) /60;
+   double *xt;
-   sec_left = (sec_left) % (60);
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   xt=vector(1,ncom);
-   return ascdiff;
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
- }
+   f=(*nrfunc)(xt);
+   free_vector(xt,1,ncom);
- /*************** powell ************************/
+   return f;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+ }
-             double (*func)(double []))
- {
+ /*****************brent *************************/
-   void linmin(double p[], double xi[], int n, double *fret,
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-               double (*func)(double []));
+ {
-   int i,ibig,j;
+   int iter;
-   double del,t,*pt,*ptt,*xit;
+   double a,b,d,etemp;
-   double fp,fptt;
+   double fu=0,fv,fw,fx;
-   double *xits;
+   double ftemp=0.;
-   int niterf, itmp;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   double e=0.0;
-   pt=vector(1,n);
-   ptt=vector(1,n);
+   a=(ax < cx ? ax : cx);
-   xit=vector(1,n);
+   b=(ax > cx ? ax : cx);
-   xits=vector(1,n);
+   x=w=v=bx;
-   *fret=(*func)(p);
+   fw=fv=fx=(*f)(x);
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   for (iter=1;iter<=ITMAX;iter++) {
-   for (*iter=1;;++(*iter)) {
+     xm=0.5*(a+b);
-     fp=(*fret);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-     ibig=0;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     del=0.0;
+     printf(".");fflush(stdout);
-     last_time=curr_time;
+     fprintf(ficlog,".");fflush(ficlog);
-     (void) gettimeofday(&curr_time,&tzp);
+ #ifdef DEBUGBRENT
-     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);
+     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,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+     fprintf(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);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-    for (i=1;i<=n;i++) {
+ #endif
-       printf(" %d %.12f",i, p[i]);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+       *xmin=x;
-       fprintf(ficrespow," %.12lf", p[i]);
+       return fx;
      }
-     printf("\n");
+     ftemp=fu;
-     fprintf(ficlog,"\n");
+     if (fabs(e) > tol1) {
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+       r=(x-w)*(fx-fv);
-     if(*iter <=3){
+       q=(x-v)*(fx-fw);
-       tm = *localtime(&curr_time.tv_sec);
+       p=(x-v)*q-(x-w)*r;
-       strcpy(strcurr,asctime(&tm));
+       q=2.0*(q-r);
- /*       asctime_r(&tm,strcurr); */
+       if (q > 0.0) p = -p;
-       forecast_time=curr_time;
+       q=fabs(q);
-       itmp = strlen(strcurr);
+       etemp=e;
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+       e=d;
-         strcurr[itmp-1]='\0';
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       else {
-       for(niterf=10;niterf<=30;niterf+=10){
+         d=p/q;
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         u=x+d;
-         tmf = *localtime(&forecast_time.tv_sec);
+         if (u-a < tol2 || b-u < tol2)
- /*      asctime_r(&tmf,strfor); */
+           d=SIGN(tol1,xm-x);
-         strcpy(strfor,asctime(&tmf));
+       }
-         itmp = strlen(strfor);
+     } else {
-         if(strfor[itmp-1]=='\n')
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         strfor[itmp-1]='\0';
+     }
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-         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);
+     fu=(*f)(u);
-       }
+     if (fu <= fx) {
-     }
+       if (u >= x) a=x; else b=x;
-     for (i=1;i<=n;i++) {
+       SHFT(v,w,x,u)
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+         SHFT(fv,fw,fx,fu)
-       fptt=(*fret);
+         } else {
- #ifdef DEBUG
+           if (u < x) a=u; else b=u;
-       printf("fret=%lf \n",*fret);
+           if (fu <= fw || w == x) {
-       fprintf(ficlog,"fret=%lf \n",*fret);
+             v=w;
- #endif
+             w=u;
-       printf("%d",i);fflush(stdout);
+             fv=fw;
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+             fw=fu;
-       linmin(p,xit,n,fret,func);
+           } else if (fu <= fv || v == x || v == w) {
-       if (fabs(fptt-(*fret)) > del) {
+             v=u;
-         del=fabs(fptt-(*fret));
+             fv=fu;
-         ibig=i;
+           }
-       }
+         }
- #ifdef DEBUG
+   }
-       printf("%d %.12e",i,(*fret));
+   nrerror("Too many iterations in brent");
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   *xmin=x;
-       for (j=1;j<=n;j++) {
+   return fx;
-         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]);
+ /****************** mnbrak ***********************/
-       }
-       for(j=1;j<=n;j++) {
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         printf(" p=%.12e",p[j]);
+             double (*func)(double))
-         fprintf(ficlog," p=%.12e",p[j]);
+ {
-       }
+   double ulim,u,r,q, dum;
-       printf("\n");
+   double fu;
-       fprintf(ficlog,"\n");
- #endif
+   *fa=(*func)(*ax);
-     }
+   *fb=(*func)(*bx);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   if (*fb > *fa) {
- #ifdef DEBUG
+     SHFT(dum,*ax,*bx,dum)
-       int k[2],l;
+       SHFT(dum,*fb,*fa,dum)
-       k[0]=1;
+       }
-       k[1]=-1;
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       printf("Max: %.12e",(*func)(p));
+   *fc=(*func)(*cx);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   while (*fb > *fc) { /* Declining fa, fb, fc */
-       for (j=1;j<=n;j++) {
+     r=(*bx-*ax)*(*fb-*fc);
-         printf(" %.12e",p[j]);
+     q=(*bx-*cx)*(*fb-*fa);
-         fprintf(ficlog," %.12e",p[j]);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       }
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-       printf("\n");
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-       fprintf(ficlog,"\n");
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
-       for(l=0;l<=1;l++) {
+       fu=(*func)(u);
-         for (j=1;j<=n;j++) {
+ #ifdef DEBUG
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       /* f(x)=A(x-u)**2+f(u) */
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       double A, fparabu;
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         }
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       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);
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       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);
-       }
+ #endif
- #endif
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+       fu=(*func)(u);
+       if (fu < *fc) {
-       free_vector(xit,1,n);
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-       free_vector(xits,1,n);
+           SHFT(*fb,*fc,fu,(*func)(u))
-       free_vector(ptt,1,n);
+           }
-       free_vector(pt,1,n);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-       return;
+       u=ulim;
-     }
+       fu=(*func)(u);
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     } else {
-     for (j=1;j<=n;j++) {
+       u=(*cx)+GOLD*(*cx-*bx);
-       ptt[j]=2.0*p[j]-pt[j];
+       fu=(*func)(u);
-       xit[j]=p[j]-pt[j];
+     }
-       pt[j]=p[j];
+     SHFT(*ax,*bx,*cx,u)
-     }
+       SHFT(*fa,*fb,*fc,fu)
-     fptt=(*func)(ptt);
+       }
-     if (fptt < fp) {
+ }
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-       if (t < 0.0) {
+ /*************** linmin ************************/
-         linmin(p,xit,n,fret,func);
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-         for (j=1;j<=n;j++) {
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-           xi[j][ibig]=xi[j][n];
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-           xi[j][n]=xit[j];
+ the value of func at the returned location p . This is actually all accomplished by calling the
-         }
+ routines mnbrak and brent .*/
- #ifdef DEBUG
+ int ncom;
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ double *pcom,*xicom;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ double (*nrfunc)(double []);
-         for(j=1;j<=n;j++){
-           printf(" %.12e",xit[j]);
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-           fprintf(ficlog," %.12e",xit[j]);
+ {
-         }
+   double brent(double ax, double bx, double cx,
-         printf("\n");
+                double (*f)(double), double tol, double *xmin);
-         fprintf(ficlog,"\n");
+   double f1dim(double x);
- #endif
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-       }
+               double *fc, double (*func)(double));
-     }
+   int j;
-   }
+   double xx,xmin,bx,ax;
- }
+   double fx,fb,fa;
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   ncom=n;
+   pcom=vector(1,n);
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   xicom=vector(1,n);
- {
+   nrfunc=func;
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   for (j=1;j<=n;j++) {
-      matrix by transitions matrix until convergence is reached */
+     pcom[j]=p[j];
+     xicom[j]=xi[j];
-   int i, ii,j,k;
+   }
-   double min, max, maxmin, maxmax,sumnew=0.;
+   ax=0.0;
-   double **matprod2();
+   xx=1.0;
-   double **out, cov[NCOVMAX], **pmij();
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
-   double **newm;
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+ #ifdef DEBUG
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     for (j=1;j<=nlstate+ndeath;j++){
+ #endif
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   for (j=1;j<=n;j++) {
-     }
+     xi[j] *= xmin;
+     p[j] += xi[j];
-    cov[1]=1.;
+   }
+   free_vector(xicom,1,n);
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   free_vector(pcom,1,n);
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ }
-     newm=savm;
-     /* Covariates have to be included here again */
-      cov[2]=agefin;
+ /*************** powell ************************/
+ /*
-       for (k=1; k<=cptcovn;k++) {
+ Minimization of a function func of n variables. Input consists of an initial starting point
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-         /*      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]]);*/
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-       }
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-       for (k=1; k<=cptcovprod;k++)
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+  */
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+             double (*func)(double []))
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+ {
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   void linmin(double p[], double xi[], int n, double *fret,
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+               double (*func)(double []));
+   int i,ibig,j;
-     savm=oldm;
+   double del,t,*pt,*ptt,*xit;
-     oldm=newm;
+   double fp,fptt;
-     maxmax=0.;
+   double *xits;
-     for(j=1;j<=nlstate;j++){
+   int niterf, itmp;
-       min=1.;
-       max=0.;
+   pt=vector(1,n);
-       for(i=1; i<=nlstate; i++) {
+   ptt=vector(1,n);
-         sumnew=0;
+   xit=vector(1,n);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+   xits=vector(1,n);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+   *fret=(*func)(p);
-         max=FMAX(max,prlim[i][j]);
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         min=FMIN(min,prlim[i][j]);
+     rcurr_time = time(NULL);
-       }
+   for (*iter=1;;++(*iter)) {
-       maxmin=max-min;
+     fp=(*fret);
-       maxmax=FMAX(maxmax,maxmin);
+     ibig=0;
-     }
+     del=0.0;
-     if(maxmax < ftolpl){
+     rlast_time=rcurr_time;
-       return prlim;
+     /* (void) gettimeofday(&curr_time,&tzp); */
-     }
+     rcurr_time = time(NULL);
-   }
+     curr_time = *localtime(&rcurr_time);
- }
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
- /*************** transition probabilities ***************/
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+    for (i=1;i<=n;i++) {
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       printf(" %d %.12f",i, p[i]);
- {
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-   double s1, s2;
+       fprintf(ficrespow," %.12lf", p[i]);
-   /*double t34;*/
+     }
-   int i,j,j1, nc, ii, jj;
+     printf("\n");
+     fprintf(ficlog,"\n");
-     for(i=1; i<= nlstate; i++){
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-       for(j=1; j<i;j++){
+     if(*iter <=3){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       tml = *localtime(&rcurr_time);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       strcpy(strcurr,asctime(&tml));
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       rforecast_time=rcurr_time;
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+       itmp = strlen(strcurr);
-         }
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-         ps[i][j]=s2;
+         strcurr[itmp-1]='\0';
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       }
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       for(niterf=10;niterf<=30;niterf+=10){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+         forecast_time = *localtime(&rforecast_time);
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         strcpy(strfor,asctime(&forecast_time));
-         }
+         itmp = strlen(strfor);
-         ps[i][j]=s2;
+         if(strfor[itmp-1]=='\n')
-       }
+         strfor[itmp-1]='\0';
-     }
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-     /*ps[3][2]=1;*/
+         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);
+       }
-     for(i=1; i<= nlstate; i++){
+     }
-       s1=0;
+     for (i=1;i<=n;i++) {
-       for(j=1; j<i; j++)
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-         s1+=exp(ps[i][j]);
+       fptt=(*fret);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ #ifdef DEBUG
-         s1+=exp(ps[i][j]);
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       ps[i][i]=1./(s1+1.);
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       for(j=1; j<i; j++)
+ #endif
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       printf("%d",i);fflush(stdout);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       linmin(p,xit,n,fret,func);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       if (fabs(fptt-(*fret)) > del) {
-     } /* end i */
+         del=fabs(fptt-(*fret));
+         ibig=i;
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+ #ifdef DEBUG
-         ps[ii][jj]=0;
+       printf("%d %.12e",i,(*fret));
-         ps[ii][ii]=1;
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       }
+       for (j=1;j<=n;j++) {
-     }
+         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]);
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       }
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       for(j=1;j<=n;j++) {
- /*         printf("ddd %lf ",ps[ii][jj]); */
+         printf(" p(%d)=%.12e",j,p[j]);
- /*       } */
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
- /*       printf("\n "); */
+       }
- /*        } */
+       printf("\n");
- /*        printf("\n ");printf("%lf ",cov[2]); */
+       fprintf(ficlog,"\n");
-        /*
+ #endif
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     } /* end i */
-       goto end;*/
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-     return ps;
+ #ifdef DEBUG
- }
+       int k[2],l;
+       k[0]=1;
- /**************** Product of 2 matrices ******************/
+       k[1]=-1;
+       printf("Max: %.12e",(*func)(p));
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
- {
+       for (j=1;j<=n;j++) {
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+         printf(" %.12e",p[j]);
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+         fprintf(ficlog," %.12e",p[j]);
-   /* in, b, out are matrice of pointers which should have been initialized
+       }
-      before: only the contents of out is modified. The function returns
+       printf("\n");
-      a pointer to pointers identical to out */
+       fprintf(ficlog,"\n");
-   long i, j, k;
+       for(l=0;l<=1;l++) {
-   for(i=nrl; i<= nrh; i++)
+         for (j=1;j<=n;j++) {
-     for(k=ncolol; k<=ncoloh; k++)
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-         out[i][k] +=in[i][j]*b[j][k];
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+         }
-   return out;
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
- }
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       }
+ #endif
- /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       free_vector(xit,1,n);
- {
+       free_vector(xits,1,n);
-   /* Computes the transition matrix starting at age 'age' over
+       free_vector(ptt,1,n);
-      'nhstepm*hstepm*stepm' months (i.e. until
+       free_vector(pt,1,n);
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       return;
-      nhstepm*hstepm matrices.
+     }
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-      (typically every 2 years instead of every month which is too big
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
-      for the memory).
+       ptt[j]=2.0*p[j]-pt[j];
-      Model is determined by parameters x and covariates have to be
+       xit[j]=p[j]-pt[j];
-      included manually here.
+       pt[j]=p[j];
+     }
-      */
+     fptt=(*func)(ptt);
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-   int i, j, d, h, k;
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-   double **out, cov[NCOVMAX];
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-   double **newm;
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-   /* Hstepm could be zero and should return the unit matrix */
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-   for (i=1;i<=nlstate+ndeath;i++)
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
-     for (j=1;j<=nlstate+ndeath;j++){
+       /* Thus we compare delta(2h) with observed f1-f3 */
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       /* or best gain on one ancient line 'del' with total  */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
-     }
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(h=1; h <=nhstepm; h++){
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-     for(d=1; d <=hstepm; d++){
+       t= t- del*SQR(fp-fptt);
-       newm=savm;
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-       /* Covariates have to be included here again */
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-       cov[1]=1.;
+ #ifdef DEBUG
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       for (k=1; k<=cptcovage;k++)
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       for (k=1; k<=cptcovprod;k++)
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+ #endif
+       if (t < 0.0) { /* Then we use it for last direction */
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
-       /*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,
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
-       savm=oldm;
+         }
-       oldm=newm;
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-     }
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-     for(i=1; i<=nlstate+ndeath; i++)
-       for(j=1;j<=nlstate+ndeath;j++) {
+ #ifdef DEBUG
-         po[i][j][h]=newm[i][j];
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-          */
+         for(j=1;j<=n;j++){
-       }
+           printf(" %.12e",xit[j]);
-   } /* end h */
+           fprintf(ficlog," %.12e",xit[j]);
-   return po;
+         }
- }
+         printf("\n");
+         fprintf(ficlog,"\n");
+ #endif
- /*************** log-likelihood *************/
+       } /* end of t negative */
- double func( double *x)
+     } /* end if (fptt < fp)  */
- {
+   }
-   int i, ii, j, k, mi, d, kk;
+ }
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
-   double **out;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   double sw; /* Sum of weights */
-   double lli; /* Individual log likelihood */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-   int s1, s2;
+ {
-   double bbh, survp;
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-   long ipmx;
+      matrix by transitions matrix until convergence is reached */
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+   int i, ii,j,k;
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   double min, max, maxmin, maxmax,sumnew=0.;
-   /*for(i=1;i<imx;i++)
+   /* double **matprod2(); */ /* test */
-     printf(" %d\n",s[4][i]);
+   double **out, cov[NCOVMAX+1], **pmij();
-   */
+   double **newm;
-   cov[1]=1.;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (j=1;j<=nlstate+ndeath;j++){
-   if(mle==1){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+   cov[1]=1.;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     newm=savm;
-           }
+     /* Covariates have to be included here again */
-         for(d=0; d<dh[mi][i]; d++){
+     cov[2]=agefin;
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     for (k=1; k<=cptcovn;k++) {
-           for (kk=1; kk<=cptcovage;kk++) {
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       /*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]]);*/
-           }
+     }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-           savm=oldm;
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-           oldm=newm;
-         } /* end mult */
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     savm=oldm;
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+     oldm=newm;
-          * probability in order to take into account the bias as a fraction of the way
+     maxmax=0.;
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+     for(j=1;j<=nlstate;j++){
-          * -stepm/2 to stepm/2 .
+       min=1.;
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       max=0.;
-          * For stepm > 1 the results are less biased than in previous versions.
+       for(i=1; i<=nlstate; i++) {
-          */
+         sumnew=0;
-         s1=s[mw[mi][i]][i];
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         s2=s[mw[mi+1][i]][i];
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-         bbh=(double)bh[mi][i]/(double)stepm;
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-         /* bias bh is positive if real duration
+         max=FMAX(max,prlim[i][j]);
-          * is higher than the multiple of stepm and negative otherwise.
+         min=FMIN(min,prlim[i][j]);
-          */
+       }
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+       maxmin=max-min;
-         if( s2 > nlstate){
+       maxmax=FMAX(maxmax,maxmin);
-           /* i.e. if s2 is a death state and if the date of death is known
+     } /* j loop */
-              then the contribution to the likelihood is the probability to
+     if(maxmax < ftolpl){
-              die between last step unit time and current  step unit time,
+       return prlim;
-              which is also equal to probability to die before dh
+     }
-              minus probability to die before dh-stepm .
+   } /* age loop */
-              In version up to 0.92 likelihood was computed
+   return prlim; /* should not reach here */
-         as if date of death was unknown. Death was treated as any other
+ }
-         health state: the date of the interview describes the actual state
-         and not the date of a change in health state. The former idea was
+ /*************** transition probabilities ***************/
-         to consider that at each interview the state was recorded
-         (healthy, disable or death) and IMaCh was corrected; but when we
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-         introduced the exact date of death then we should have modified
+ {
-         the contribution of an exact death to the likelihood. This new
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-         contribution is smaller and very dependent of the step unit
+      computes the probability to be observed in state j being in state i by appying the
-         stepm. It is no more the probability to die between last interview
+      model to the ncovmodel covariates (including constant and age).
-         and month of death but the probability to survive from last
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         interview up to one month before death multiplied by the
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         probability to die within a month. Thanks to Chris
+      ncth covariate in the global vector x is given by the formula:
-         Jackson for correcting this bug.  Former versions increased
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-         mortality artificially. The bad side is that we add another loop
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-         which slows down the processing. The difference can be up to 10%
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         lower mortality.
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-           */
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-           lli=log(out[s1][s2] - savm[s1][s2]);
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
-         } else if  (s2==-2) {
+   /*double t34;*/
-           for (j=1,survp=0. ; j<=nlstate; j++)
+   int i,j, nc, ii, jj;
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           /*survp += out[s1][j]; */
+     for(i=1; i<= nlstate; i++){
-           lli= log(survp);
+       for(j=1; j<i;j++){
-         }
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         else if  (s2==-4) {
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-           for (j=3,survp=0. ; j<=nlstate; j++)
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         }
-           lli= log(survp);
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         }
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
-         else if  (s2==-5) {
+       for(j=i+1; j<=nlstate+ndeath;j++){
-           for (j=1,survp=0. ; j<=2; j++)
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-           lli= log(survp);
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         }
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+         }
-         else{
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-           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 */
+     }
-         }
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+     for(i=1; i<= nlstate; i++){
-         /*if(lli ==000.0)*/
+       s1=0;
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+       for(j=1; j<i; j++){
-         ipmx +=1;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         sw += weight[i];
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       }
-       } /* end of wave */
+       for(j=i+1; j<=nlstate+ndeath; j++){
-     } /* end of individual */
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   }  else if(mle==2){
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       ps[i][i]=1./(s1+1.);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* Computing other pijs */
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(j=1; j<i; j++)
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(j=i+1; j<=nlstate+ndeath; j++)
-           }
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         for(d=0; d<=dh[mi][i]; d++){
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-           newm=savm;
+     } /* end i */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-           }
+         ps[ii][jj]=0;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         ps[ii][ii]=1;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       }
-           savm=oldm;
+     }
-           oldm=newm;
-         } /* end mult */
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         s1=s[mw[mi][i]][i];
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-         s2=s[mw[mi+1][i]][i];
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         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 */
+     /*   printf("\n "); */
-         ipmx +=1;
+     /* } */
-         sw += weight[i];
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     /*
-       } /* end of wave */
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-     } /* end of individual */
+       goto end;*/
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+     return ps;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+ /**************** Product of 2 matrices ******************/
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ {
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-           }
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         for(d=0; d<dh[mi][i]; d++){
+   /* in, b, out are matrice of pointers which should have been initialized
-           newm=savm;
+      before: only the contents of out is modified. The function returns
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+      a pointer to pointers identical to out */
-           for (kk=1; kk<=cptcovage;kk++) {
+   int i, j, k;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   for(i=nrl; i<= nrh; i++)
-           }
+     for(k=ncolol; k<=ncoloh; k++){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       out[i][k]=0.;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for(j=ncl; j<=nch; j++)
-           savm=oldm;
+         out[i][k] +=in[i][j]*b[j][k];
-           oldm=newm;
+     }
-         } /* end mult */
+   return out;
+ }
-         s1=s[mw[mi][i]][i];
-         s2=s[mw[mi+1][i]][i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+ /************* Higher Matrix Product ***************/
-         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;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-         sw += weight[i];
+ {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /* Computes the transition matrix starting at age 'age' over
-       } /* end of wave */
+      'nhstepm*hstepm*stepm' months (i.e. until
-     } /* end of individual */
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+      nhstepm*hstepm matrices.
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      (typically every 2 years instead of every month which is too big
-       for(mi=1; mi<= wav[i]-1; mi++){
+      for the memory).
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+      Model is determined by parameters x and covariates have to be
-           for (j=1;j<=nlstate+ndeath;j++){
+      included manually here.
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+      */
-           }
-         for(d=0; d<dh[mi][i]; d++){
+   int i, j, d, h, k;
-           newm=savm;
+   double **out, cov[NCOVMAX+1];
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   double **newm;
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   /* Hstepm could be zero and should return the unit matrix */
-           }
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-           savm=oldm;
+     }
-           oldm=newm;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         } /* end mult */
+   for(h=1; h <=nhstepm; h++){
+     for(d=1; d <=hstepm; d++){
-         s1=s[mw[mi][i]][i];
+       newm=savm;
-         s2=s[mw[mi+1][i]][i];
+       /* Covariates have to be included here again */
-         if( s2 > nlstate){
+       cov[1]=1.;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-         }else{
+       for (k=1; k<=cptcovn;k++)
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         }
+       for (k=1; k<=cptcovage;k++)
-         ipmx +=1;
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         sw += weight[i];
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-       } /* end of wave */
-     } /* end of individual */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-       for(mi=1; mi<= wav[i]-1; mi++){
+       savm=oldm;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       oldm=newm;
-           for (j=1;j<=nlstate+ndeath;j++){
+     }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for(i=1; i<=nlstate+ndeath; i++)
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(j=1;j<=nlstate+ndeath;j++) {
-           }
+         po[i][j][h]=newm[i][j];
-         for(d=0; d<dh[mi][i]; d++){
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-           newm=savm;
+       }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /*printf("h=%d ",h);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+   } /* end h */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ /*     printf("\n H=%d \n",h); */
-           }
+   return po;
+ }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #ifdef NLOPT
-           savm=oldm;
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-           oldm=newm;
+   double fret;
-         } /* end mult */
+   double *xt;
+   int j;
-         s1=s[mw[mi][i]][i];
+   myfunc_data *d2 = (myfunc_data *) pd;
-         s2=s[mw[mi+1][i]][i];
+ /* xt = (p1-1); */
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+   xt=vector(1,n);
-         ipmx +=1;
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-         sw += weight[i];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-         /*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]);*/
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-       } /* end of wave */
+   printf("Function = %.12lf ",fret);
-     } /* end of individual */
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   } /* End of if */
+   printf("\n");
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+  free_vector(xt,1,n);
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   return fret;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ }
-   return -l;
+ #endif
- }
+ /*************** log-likelihood *************/
- /*************** log-likelihood *************/
+ double func( double *x)
- double funcone( double *x)
+ {
- {
+   int i, ii, j, k, mi, d, kk;
-   /* Same as likeli but slower because of a lot of printf and if */
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   int i, ii, j, k, mi, d, kk;
+   double **out;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double sw; /* Sum of weights */
-   double **out;
+   double lli; /* Individual log likelihood */
-   double lli; /* Individual log likelihood */
+   int s1, s2;
-   double llt;
+   double bbh, survp;
-   int s1, s2;
+   long ipmx;
-   double bbh, survp;
+   /*extern weight */
-   /*extern weight */
+   /* We are differentiating ll according to initial status */
-   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
-   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
-     printf(" %d\n",s[4][i]);
+   */
-   */
-   cov[1]=1.;
+   ++countcallfunc;
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   cov[1]=1.;
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     for(mi=1; mi<= wav[i]-1; mi++){
+   if(mle==1){
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         for (j=1;j<=nlstate+ndeath;j++){
+       /* Computes the values of the ncovmodel covariates of the model
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-         }
+          to be observed in j being in i according to the model.
-       for(d=0; d<dh[mi][i]; d++){
+        */
-         newm=savm;
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         cov[2+k]=covar[Tvar[k]][i];
-         for (kk=1; kk<=cptcovage;kk++) {
+       }
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-         }
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+          has been calculated etc */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for(mi=1; mi<= wav[i]-1; mi++){
-         savm=oldm;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         oldm=newm;
+           for (j=1;j<=nlstate+ndeath;j++){
-       } /* end mult */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       s1=s[mw[mi][i]][i];
+           }
-       s2=s[mw[mi+1][i]][i];
+         for(d=0; d<dh[mi][i]; d++){
-       bbh=(double)bh[mi][i]/(double)stepm;
+           newm=savm;
-       /* bias is positive if real duration
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-        * is higher than the multiple of stepm and negative otherwise.
+           for (kk=1; kk<=cptcovage;kk++) {
-        */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+           }
-         lli=log(out[s1][s2] - savm[s1][s2]);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       } else if  (s2==-2) {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         for (j=1,survp=0. ; j<=nlstate; j++)
+           savm=oldm;
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           oldm=newm;
-         lli= log(survp);
+         } /* end mult */
-       }else if (mle==1){
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-       } else if(mle==2){
+         /* But now since version 0.9 we anticipate for bias at large 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 */
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-       } else if(mle==3){  /* exponential inter-extrapolation */
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         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 */
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         lli=log(out[s1][s2]); /* Original formula */
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+          * probability in order to take into account the bias as a fraction of the way
-         lli=log(out[s1][s2]); /* Original formula */
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-       } /* End of if */
+          * -stepm/2 to stepm/2 .
-       ipmx +=1;
+          * For stepm=1 the results are the same as for previous versions of Imach.
-       sw += weight[i];
+          * For stepm > 1 the results are less biased than in previous versions.
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+          */
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+         s1=s[mw[mi][i]][i];
-       if(globpr){
+         s2=s[mw[mi+1][i]][i];
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         bbh=(double)bh[mi][i]/(double)stepm;
-  %11.6f %11.6f %11.6f ", \
+         /* bias bh is positive if real duration
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+          * is higher than the multiple of stepm and negative otherwise.
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+          */
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-           llt +=ll[k]*gipmx/gsw;
+         if( s2 > nlstate){
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           /* i.e. if s2 is a death state and if the date of death is known
-         }
+              then the contribution to the likelihood is the probability to
-         fprintf(ficresilk," %10.6f\n", -llt);
+              die between last step unit time and current  step unit time,
-       }
+              which is also equal to probability to die before dh
-     } /* end of wave */
+              minus probability to die before dh-stepm .
-   } /* end of individual */
+              In version up to 0.92 likelihood was computed
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         as if date of death was unknown. Death was treated as any other
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         health state: the date of the interview describes the actual state
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         and not the date of a change in health state. The former idea was
-   if(globpr==0){ /* First time we count the contributions and weights */
+         to consider that at each interview the state was recorded
-     gipmx=ipmx;
+         (healthy, disable or death) and IMaCh was corrected; but when we
-     gsw=sw;
+         introduced the exact date of death then we should have modified
-   }
+         the contribution of an exact death to the likelihood. This new
-   return -l;
+         contribution is smaller and very dependent of the step unit
- }
+         stepm. It is no more the probability to die between last interview
+         and month of death but the probability to survive from last
+         interview up to one month before death multiplied by the
- /*************** function likelione ***********/
+         probability to die within a month. Thanks to Chris
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+         Jackson for correcting this bug.  Former versions increased
- {
+         mortality artificially. The bad side is that we add another loop
-   /* This routine should help understanding what is done with
+         which slows down the processing. The difference can be up to 10%
-      the selection of individuals/waves and
+         lower mortality.
-      to check the exact contribution to the likelihood.
+           */
-      Plotting could be done.
+           lli=log(out[s1][s2] - savm[s1][s2]);
-    */
-   int k;
+         } else if  (s2==-2) {
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-     strcpy(fileresilk,"ilk");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     strcat(fileresilk,fileres);
+           /*survp += out[s1][j]; */
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+           lli= log(survp);
-       printf("Problem with resultfile: %s\n", fileresilk);
+         }
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-     }
+         else if  (s2==-4) {
-     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");
+           for (j=3,survp=0. ; j<=nlstate; j++)
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+           lli= log(survp);
-     for(k=1; k<=nlstate; k++)
+         }
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         else if  (s2==-5) {
-   }
+           for (j=1,survp=0. ; j<=2; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   *fretone=(*funcone)(p);
+           lli= log(survp);
-   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));
+         else{
-     fflush(fichtm);
+           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 */
-   return;
+         }
- }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         /*if(lli ==000.0)*/
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
- /*********** Maximum Likelihood Estimation ***************/
+         ipmx +=1;
+         sw += weight[i];
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- {
+       } /* end of wave */
-   int i,j, iter;
+     } /* end of individual */
-   double **xi;
+   }  else if(mle==2){
-   double fret;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double fretone; /* Only one call to likelihood */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   /*  char filerespow[FILENAMELENGTH];*/
+       for(mi=1; mi<= wav[i]-1; mi++){
-   xi=matrix(1,npar,1,npar);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   for (i=1;i<=npar;i++)
+           for (j=1;j<=nlstate+ndeath;j++){
-     for (j=1;j<=npar;j++)
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+           }
-   strcpy(filerespow,"pow");
+         for(d=0; d<=dh[mi][i]; d++){
-   strcat(filerespow,fileres);
+           newm=savm;
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     printf("Problem with resultfile: %s\n", filerespow);
+           for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   }
+           }
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   for (i=1;i<=nlstate;i++)
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for(j=1;j<=nlstate+ndeath;j++)
+           savm=oldm;
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+           oldm=newm;
-   fprintf(ficrespow,"\n");
+         } /* end mult */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   free_matrix(xi,1,npar,1,npar);
+         bbh=(double)bh[mi][i]/(double)stepm;
-   fclose(ficrespow);
+         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#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         ipmx +=1;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+         sw += weight[i];
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
- }
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
- /**** Computes Hessian and covariance matrix ***/
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- {
+       for(mi=1; mi<= wav[i]-1; mi++){
-   double  **a,**y,*x,pd;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   double **hess;
+           for (j=1;j<=nlstate+ndeath;j++){
-   int i, j,jk;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int *indx;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+         for(d=0; d<dh[mi][i]; d++){
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+           newm=savm;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+           for (kk=1; kk<=cptcovage;kk++) {
-   double gompertz(double p[]);
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   hess=matrix(1,npar,1,npar);
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+           savm=oldm;
-   for (i=1;i<=npar;i++){
+           oldm=newm;
-     printf("%d",i);fflush(stdout);
+         } /* end mult */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+         s1=s[mw[mi][i]][i];
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-     /*  printf(" %f ",p[i]);
+         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 */
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         ipmx +=1;
-   }
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   for (i=1;i<=npar;i++) {
+       } /* end of wave */
-     for (j=1;j<=npar;j++)  {
+     } /* end of individual */
-       if (j>i) {
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-         printf(".%d%d",i,j);fflush(stdout);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         hess[j][i]=hess[i][j];
+           for (j=1;j<=nlstate+ndeath;j++){
-         /*printf(" %lf ",hess[i][j]);*/
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     }
+           }
-   }
+         for(d=0; d<dh[mi][i]; d++){
-   printf("\n");
+           newm=savm;
-   fprintf(ficlog,"\n");
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+           }
-   a=matrix(1,npar,1,npar);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   y=matrix(1,npar,1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   x=vector(1,npar);
+           savm=oldm;
-   indx=ivector(1,npar);
+           oldm=newm;
-   for (i=1;i<=npar;i++)
+         } /* end mult */
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   ludcmp(a,npar,indx,&pd);
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   for (j=1;j<=npar;j++) {
+         if( s2 > nlstate){
-     for (i=1;i<=npar;i++) x[i]=0;
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     x[j]=1;
+         }else{
-     lubksb(a,npar,indx,x);
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-     for (i=1;i<=npar;i++){
+         }
-       matcov[i][j]=x[i];
+         ipmx +=1;
-     }
+         sw += weight[i];
-   }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-   printf("\n#Hessian matrix#\n");
+       } /* end of wave */
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+     } /* end of individual */
-   for (i=1;i<=npar;i++) {
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-     for (j=1;j<=npar;j++) {
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       printf("%.3e ",hess[i][j]);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+       for(mi=1; mi<= wav[i]-1; mi++){
-     }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     printf("\n");
+           for (j=1;j<=nlstate+ndeath;j++){
-     fprintf(ficlog,"\n");
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   /* Recompute Inverse */
+         for(d=0; d<dh[mi][i]; d++){
-   for (i=1;i<=npar;i++)
+           newm=savm;
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   ludcmp(a,npar,indx,&pd);
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   /*  printf("\n#Hessian matrix recomputed#\n");
+           }
-   for (j=1;j<=npar;j++) {
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     for (i=1;i<=npar;i++) x[i]=0;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     x[j]=1;
+           savm=oldm;
-     lubksb(a,npar,indx,x);
+           oldm=newm;
-     for (i=1;i<=npar;i++){
+         } /* end mult */
-       y[i][j]=x[i];
-       printf("%.3e ",y[i][j]);
+         s1=s[mw[mi][i]][i];
-       fprintf(ficlog,"%.3e ",y[i][j]);
+         s2=s[mw[mi+1][i]][i];
-     }
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-     printf("\n");
+         ipmx +=1;
-     fprintf(ficlog,"\n");
+         sw += weight[i];
-   }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   */
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+       } /* end of wave */
-   free_matrix(a,1,npar,1,npar);
+     } /* end of individual */
-   free_matrix(y,1,npar,1,npar);
+   } /* End of if */
-   free_vector(x,1,npar);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   free_ivector(indx,1,npar);
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   free_matrix(hess,1,npar,1,npar);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
+ }
- }
+ /*************** log-likelihood *************/
- /*************** hessian matrix ****************/
+ double funcone( double *x)
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+ {
- {
+   /* Same as likeli but slower because of a lot of printf and if */
-   int i;
+   int i, ii, j, k, mi, d, kk;
-   int l=1, lmax=20;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   double k1,k2;
+   double **out;
-   double p2[NPARMAX+1];
+   double lli; /* Individual log likelihood */
-   double res;
+   double llt;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   int s1, s2;
-   double fx;
+   double bbh, survp;
-   int k=0,kmax=10;
+   /*extern weight */
-   double l1;
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   fx=func(x);
+   /*for(i=1;i<imx;i++)
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+     printf(" %d\n",s[4][i]);
-   for(l=0 ; l <=lmax; l++){
+   */
-     l1=pow(10,l);
+   cov[1]=1.;
-     delts=delt;
-     for(k=1 ; k <kmax; k=k+1){
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-       delt = delta*(l1*k);
-       p2[theta]=x[theta] +delt;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       k1=func(p2)-fx;
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       p2[theta]=x[theta]-delt;
+     for(mi=1; mi<= wav[i]-1; mi++){
-       k2=func(p2)-fx;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         for (j=1;j<=nlstate+ndeath;j++){
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
- #ifdef DEBUG
+         }
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       for(d=0; d<dh[mi][i]; d++){
-       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);
+         newm=savm;
- #endif
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+         for (kk=1; kk<=cptcovage;kk++) {
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         k=kmax;
+         }
-       }
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         k=kmax; l=lmax*10.;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       }
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-         delts=delt;
+         savm=oldm;
-       }
+         oldm=newm;
-     }
+       } /* end mult */
-   }
-   delti[theta]=delts;
+       s1=s[mw[mi][i]][i];
-   return res;
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
- }
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+        */
- {
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-   int i;
+         lli=log(out[s1][s2] - savm[s1][s2]);
-   int l=1, l1, lmax=20;
+       } else if  (s2==-2) {
-   double k1,k2,k3,k4,res,fx;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   double p2[NPARMAX+1];
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   int k;
+         lli= log(survp);
+       }else if (mle==1){
-   fx=func(x);
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   for (k=1; k<=2; k++) {
+       } else if(mle==2){
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       } else if(mle==3){  /* exponential inter-extrapolation */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-     k1=func(p2)-fx;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       } else{  /* mle=0 back to 1 */
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     k2=func(p2)-fx;
+         /*lli=log(out[s1][s2]); */ /* Original formula */
+       } /* End of if */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       ipmx +=1;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+       sw += weight[i];
-     k3=func(p2)-fx;
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       if(globpr){
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     k4=func(p2)-fx;
+  %11.6f %11.6f %11.6f ", \
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
- #ifdef DEBUG
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+           llt +=ll[k]*gipmx/gsw;
- #endif
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   }
+         }
-   return res;
+         fprintf(ficresilk," %10.6f\n", -llt);
- }
+       }
+     } /* end of wave */
- /************** Inverse of matrix **************/
+   } /* end of individual */
- void ludcmp(double **a, int n, int *indx, double *d)
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
- {
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   int i,imax,j,k;
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   double big,dum,sum,temp;
+   if(globpr==0){ /* First time we count the contributions and weights */
-   double *vv;
+     gipmx=ipmx;
+     gsw=sw;
-   vv=vector(1,n);
+   }
-   *d=1.0;
+   return -l;
-   for (i=1;i<=n;i++) {
+ }
-     big=0.0;
-     for (j=1;j<=n;j++)
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+ /*************** function likelione ***********/
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     vv[i]=1.0/big;
+ {
-   }
+   /* This routine should help understanding what is done with
-   for (j=1;j<=n;j++) {
+      the selection of individuals/waves and
-     for (i=1;i<j;i++) {
+      to check the exact contribution to the likelihood.
-       sum=a[i][j];
+      Plotting could be done.
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+    */
-       a[i][j]=sum;
+   int k;
-     }
-     big=0.0;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     for (i=j;i<=n;i++) {
+     strcpy(fileresilk,"ilk");
-       sum=a[i][j];
+     strcat(fileresilk,fileres);
-       for (k=1;k<j;k++)
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-         sum -= a[i][k]*a[k][j];
+       printf("Problem with resultfile: %s\n", fileresilk);
-       a[i][j]=sum;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+     }
-         big=dum;
+     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");
-         imax=i;
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-       }
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-     }
+     for(k=1; k<=nlstate; k++)
-     if (j != imax) {
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-       for (k=1;k<=n;k++) {
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-         dum=a[imax][k];
+   }
-         a[imax][k]=a[j][k];
-         a[j][k]=dum;
+   *fretone=(*funcone)(p);
-       }
+   if(*globpri !=0){
-       *d = -(*d);
+     fclose(ficresilk);
-       vv[imax]=vv[j];
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-     }
+     fflush(fichtm);
-     indx[j]=imax;
+   }
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   return;
-     if (j != n) {
+ }
-       dum=1.0/(a[j][j]);
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-     }
+ /*********** Maximum Likelihood Estimation ***************/
-   }
-   free_vector(vv,1,n);  /* Doesn't work */
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
- ;
+ {
- }
+   int i,j, iter=0;
+   double **xi;
- void lubksb(double **a, int n, int *indx, double b[])
+   double fret;
- {
+   double fretone; /* Only one call to likelihood */
-   int i,ii=0,ip,j;
+   /*  char filerespow[FILENAMELENGTH];*/
-   double sum;
+ #ifdef NLOPT
-   for (i=1;i<=n;i++) {
+   int creturn;
-     ip=indx[i];
+   nlopt_opt opt;
-     sum=b[ip];
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-     b[ip]=b[i];
+   double *lb;
-     if (ii)
+   double minf; /* the minimum objective value, upon return */
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-     else if (sum) ii=i;
+   myfunc_data dinst, *d = &dinst;
-     b[i]=sum;
+ #endif
-   }
-   for (i=n;i>=1;i--) {
-     sum=b[i];
+   xi=matrix(1,npar,1,npar);
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   for (i=1;i<=npar;i++)
-     b[i]=sum/a[i][i];
+     for (j=1;j<=npar;j++)
-   }
+       xi[i][j]=(i==j ? 1.0 : 0.0);
- }
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   strcpy(filerespow,"pow");
- void pstamp(FILE *fichier)
+   strcat(filerespow,fileres);
- {
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+     printf("Problem with resultfile: %s\n", filerespow);
- }
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   }
- /************ Frequencies ********************/
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
- 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[])
+   for (i=1;i<=nlstate;i++)
- {  /* Some frequencies */
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   fprintf(ficrespow,"\n");
-   int first;
+ #ifdef POWELL
-   double ***freq; /* Frequencies */
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-   double *pp, **prop;
+ #endif
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   char fileresp[FILENAMELENGTH];
+ #ifdef NLOPT
+ #ifdef NEWUOA
-   pp=vector(1,nlstate);
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+ #else
-   strcpy(fileresp,"p");
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-   strcat(fileresp,fileres);
+ #endif
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   lb=vector(0,npar-1);
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   nlopt_set_lower_bounds(opt, lb);
-     exit(0);
+   nlopt_set_initial_step1(opt, 0.1);
-   }
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   j1=0;
+   d->function = func;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   j=cptcoveff;
+   nlopt_set_min_objective(opt, myfunc, d);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   nlopt_set_xtol_rel(opt, ftol);
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-   first=1;
+     printf("nlopt failed! %d\n",creturn);
+   }
-   for(k1=1; k1<=j;k1++){
+   else {
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-       j1++;
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+     iter=1; /* not equal */
-         scanf("%d", i);*/
+   }
-       for (i=-5; i<=nlstate+ndeath; i++)
+   nlopt_destroy(opt);
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+ #endif
-           for(m=iagemin; m <= iagemax+3; m++)
+   free_matrix(xi,1,npar,1,npar);
-             freq[i][jk][m]=0;
+   fclose(ficrespow);
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     for (i=1; i<=nlstate; i++)
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-       for(m=iagemin; m <= iagemax+3; m++)
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-         prop[i][m]=0;
+ }
-       dateintsum=0;
-       k2cpt=0;
+ /**** Computes Hessian and covariance matrix ***/
-       for (i=1; i<=imx; i++) {
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-         bool=1;
+ {
-         if  (cptcovn>0) {
+   double  **a,**y,*x,pd;
-           for (z1=1; z1<=cptcoveff; z1++)
+   double **hess;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   int i, j;
-               bool=0;
+   int *indx;
-         }
-         if (bool==1){
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-           for(m=firstpass; m<=lastpass; m++){
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-             k2=anint[m][i]+(mint[m][i]/12.);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   double gompertz(double p[]);
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   hess=matrix(1,npar,1,npar);
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               if (m<lastpass) {
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+   for (i=1;i<=npar;i++){
-               }
+     printf("%d",i);fflush(stdout);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-                 dateintsum=dateintsum+k2;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-                 k2cpt++;
-               }
+     /*  printf(" %f ",p[i]);
-               /*}*/
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-           }
+   }
-         }
-       }
+   for (i=1;i<=npar;i++) {
+     for (j=1;j<=npar;j++)  {
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       if (j>i) {
-       pstamp(ficresp);
+         printf(".%d%d",i,j);fflush(stdout);
-       if  (cptcovn>0) {
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-         fprintf(ficresp, "\n#********** Variable ");
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresp, "**********\n#");
+         hess[j][i]=hess[i][j];
-       }
+         /*printf(" %lf ",hess[i][j]);*/
-       for(i=1; i<=nlstate;i++)
+       }
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+     }
-       fprintf(ficresp, "\n");
+   }
+   printf("\n");
-       for(i=iagemin; i <= iagemax+3; i++){
+   fprintf(ficlog,"\n");
-         if(i==iagemax+3){
-           fprintf(ficlog,"Total");
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-         }else{
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-           if(first==1){
-             first=0;
+   a=matrix(1,npar,1,npar);
-             printf("See log file for details...\n");
+   y=matrix(1,npar,1,npar);
-           }
+   x=vector(1,npar);
-           fprintf(ficlog,"Age %d", i);
+   indx=ivector(1,npar);
-         }
+   for (i=1;i<=npar;i++)
-         for(jk=1; jk <=nlstate ; jk++){
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   ludcmp(a,npar,indx,&pd);
-             pp[jk] += freq[jk][m][i];
-         }
+   for (j=1;j<=npar;j++) {
-         for(jk=1; jk <=nlstate ; jk++){
+     for (i=1;i<=npar;i++) x[i]=0;
-           for(m=-1, pos=0; m <=0 ; m++)
+     x[j]=1;
-             pos += freq[jk][m][i];
+     lubksb(a,npar,indx,x);
-           if(pp[jk]>=1.e-10){
+     for (i=1;i<=npar;i++){
-             if(first==1){
+       matcov[i][j]=x[i];
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     }
-             }
+   }
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           }else{
+   printf("\n#Hessian matrix#\n");
-             if(first==1)
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (i=1;i<=npar;i++) {
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     for (j=1;j<=npar;j++) {
-           }
+       printf("%.3e ",hess[i][j]);
-         }
+       fprintf(ficlog,"%.3e ",hess[i][j]);
+     }
-         for(jk=1; jk <=nlstate ; jk++){
+     printf("\n");
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+     fprintf(ficlog,"\n");
-             pp[jk] += freq[jk][m][i];
+   }
-         }
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+   /* Recompute Inverse */
-           pos += pp[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++){
-           if(pos>=1.e-5){
+   /*  printf("\n#Hessian matrix recomputed#\n");
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   for (j=1;j<=npar;j++) {
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     for (i=1;i<=npar;i++) x[i]=0;
-           }else{
+     x[j]=1;
-             if(first==1)
+     lubksb(a,npar,indx,x);
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+     for (i=1;i<=npar;i++){
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+       y[i][j]=x[i];
-           }
+       printf("%.3e ",y[i][j]);
-           if( i <= iagemax){
+       fprintf(ficlog,"%.3e ",y[i][j]);
-             if(pos>=1.e-5){
+     }
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+     printf("\n");
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+     fprintf(ficlog,"\n");
-               /*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
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   free_matrix(a,1,npar,1,npar);
-           }
+   free_matrix(y,1,npar,1,npar);
-         }
+   free_vector(x,1,npar);
+   free_ivector(indx,1,npar);
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+   free_matrix(hess,1,npar,1,npar);
-           for(m=-1; m <=nlstate+ndeath; m++)
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+ }
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+ /*************** hessian matrix ****************/
-             }
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-         if(i <= iagemax)
+ {
-           fprintf(ficresp,"\n");
+   int i;
-         if(first==1)
+   int l=1, lmax=20;
-           printf("Others in log...\n");
+   double k1,k2;
-         fprintf(ficlog,"\n");
+   double p2[MAXPARM+1]; /* identical to x */
-       }
+   double res;
-     }
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   }
+   double fx;
-   dateintmean=dateintsum/k2cpt;
+   int k=0,kmax=10;
+   double l1;
-   fclose(ficresp);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   fx=func(x);
-   free_vector(pp,1,nlstate);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   /* End of Freq */
+     l1=pow(10,l);
- }
+     delts=delt;
+     for(k=1 ; k <kmax; k=k+1){
- /************ Prevalence ********************/
+       delt = delta*(l1*k);
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+       p2[theta]=x[theta] +delt;
- {
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+       p2[theta]=x[theta]-delt;
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       k2=func(p2)-fx;
-      We still use firstpass and lastpass as another selection.
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   */
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+ #ifdef DEBUGHESS
-   double ***freq; /* Frequencies */
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   double *pp, **prop;
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   double pos,posprop;
+ #endif
-   double  y2; /* in fractional years */
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   int iagemin, iagemax;
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+         k=kmax;
-   iagemin= (int) agemin;
+       }
-   iagemax= (int) agemax;
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   /*pp=vector(1,nlstate);*/
+         k=kmax; l=lmax*10;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       }
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   j1=0;
+         delts=delt;
+       }
-   j=cptcoveff;
+     }
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   }
+   delti[theta]=delts;
-   for(k1=1; k1<=j;k1++){
+   return res;
-     for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
+ }
-       for (i=1; i<=nlstate; i++)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-         for(m=iagemin; m <= iagemax+3; m++)
+ {
-           prop[i][m]=0.0;
+   int i;
+   int l=1, lmax=20;
-       for (i=1; i<=imx; i++) { /* Each individual */
+   double k1,k2,k3,k4,res,fx;
-         bool=1;
+   double p2[MAXPARM+1];
-         if  (cptcovn>0) {
+   int k;
-           for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   fx=func(x);
-               bool=0;
+   for (k=1; k<=2; k++) {
-         }
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-         if (bool==1) {
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+     k1=func(p2)-fx;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-               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);
+     k2=func(p2)-fx;
-               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]]);*/
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-                 prop[s[m][i]][iagemax+3] += weight[i];
+     k3=func(p2)-fx;
-               }
-             }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-           } /* end selection of waves */
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-         }
+     k4=func(p2)-fx;
-       }
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-       for(i=iagemin; i <= iagemax+3; i++){
+ #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(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     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);
-           posprop += prop[jk][i];
+ #endif
-         }
+   }
+   return res;
-         for(jk=1; jk <=nlstate ; jk++){
+ }
-           if( i <=  iagemax){
-             if(posprop>=1.e-5){
+ /************** Inverse of matrix **************/
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+ void ludcmp(double **a, int n, int *indx, double *d)
-             }
+ {
-           }
+   int i,imax,j,k;
-         }/* end jk */
+   double big,dum,sum,temp;
-       }/* end i */
+   double *vv;
-     } /* end i1 */
-   } /* end k1 */
+   vv=vector(1,n);
+   *d=1.0;
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   for (i=1;i<=n;i++) {
-   /*free_vector(pp,1,nlstate);*/
+     big=0.0;
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+     for (j=1;j<=n;j++)
- }  /* End of prevalence */
+       if ((temp=fabs(a[i][j])) > big) big=temp;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
- /************* Waves Concatenation ***************/
+     vv[i]=1.0/big;
+   }
- 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)
+   for (j=1;j<=n;j++) {
- {
+     for (i=1;i<j;i++) {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       sum=a[i][j];
-      Death is a valid wave (if date is known).
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+       a[i][j]=sum;
-      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.
+     big=0.0;
-      */
+     for (i=j;i<=n;i++) {
+       sum=a[i][j];
-   int i, mi, m;
+       for (k=1;k<j;k++)
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+         sum -= a[i][k]*a[k][j];
-      double sum=0., jmean=0.;*/
+       a[i][j]=sum;
-   int first;
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-   int j, k=0,jk, ju, jl;
+         big=dum;
-   double sum=0.;
+         imax=i;
-   first=0;
+       }
-   jmin=1e+5;
+     }
-   jmax=-1;
+     if (j != imax) {
-   jmean=0.;
+       for (k=1;k<=n;k++) {
-   for(i=1; i<=imx; i++){
+         dum=a[imax][k];
-     mi=0;
+         a[imax][k]=a[j][k];
-     m=firstpass;
+         a[j][k]=dum;
-     while(s[m][i] <= nlstate){
+       }
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       *d = -(*d);
-         mw[++mi][i]=m;
+       vv[imax]=vv[j];
-       if(m >=lastpass)
+     }
-         break;
+     indx[j]=imax;
-       else
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-         m++;
+     if (j != n) {
-     }/* end while */
+       dum=1.0/(a[j][j]);
-     if (s[m][i] > nlstate){
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-       mi++;     /* Death is another wave */
+     }
-       /* if(mi==0)  never been interviewed correctly before death */
+   }
-          /* Only death is a correct wave */
+   free_vector(vv,1,n);  /* Doesn't work */
-       mw[mi][i]=m;
+ ;
-     }
+ }
-     wav[i]=mi;
+ void lubksb(double **a, int n, int *indx, double b[])
-     if(mi==0){
+ {
-       nbwarn++;
+   int i,ii=0,ip,j;
-       if(first==0){
+   double sum;
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-         first=1;
+   for (i=1;i<=n;i++) {
-       }
+     ip=indx[i];
-       if(first==1){
+     sum=b[ip];
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+     b[ip]=b[i];
-       }
+     if (ii)
-     } /* end mi==0 */
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   } /* End individuals */
+     else if (sum) ii=i;
+     b[i]=sum;
-   for(i=1; i<=imx; i++){
+   }
-     for(mi=1; mi<wav[i];mi++){
+   for (i=n;i>=1;i--) {
-       if (stepm <=0)
+     sum=b[i];
-         dh[mi][i]=1;
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       else{
+     b[i]=sum/a[i][i];
-         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);
-             if(j==0) j=1;  /* Survives at least one month after exam */
+ void pstamp(FILE *fichier)
-             else if(j<0){
+ {
-               nberr++;
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ }
-               j=1; /* Temporary Dangerous patch */
-               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);
+ /************ Frequencies ********************/
-               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]);
+ 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[])
-               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);
+ {  /* Some frequencies */
-             }
-             k=k+1;
+   int i, m, jk, j1, bool, z1,j;
-             if (j >= jmax){
+   int first;
-               jmax=j;
+   double ***freq; /* Frequencies */
-               ijmax=i;
+   double *pp, **prop;
-             }
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-             if (j <= jmin){
+   char fileresp[FILENAMELENGTH];
-               jmin=j;
-               ijmin=i;
+   pp=vector(1,nlstate);
-             }
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-             sum=sum+j;
+   strcpy(fileresp,"p");
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   strcat(fileresp,fileres);
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-           }
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-         }
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-         else{
+     exit(0);
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   }
- /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   j1=0;
-           k=k+1;
-           if (j >= jmax) {
+   j=cptcoveff;
-             jmax=j;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-             ijmax=i;
-           }
+   first=1;
-           else if (j <= jmin){
-             jmin=j;
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-             ijmin=i;
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
-           }
+   /*    j1++; */
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-           /*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]);*/
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-           if(j<0){
+         scanf("%d", i);*/
-             nberr++;
+       for (i=-5; i<=nlstate+ndeath; i++)
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-             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(m=iagemin; m <= iagemax+3; m++)
-           }
+             freq[i][jk][m]=0;
-           sum=sum+j;
-         }
+       for (i=1; i<=nlstate; i++)
-         jk= j/stepm;
+         for(m=iagemin; m <= iagemax+3; m++)
-         jl= j -jk*stepm;
+           prop[i][m]=0;
-         ju= j -(jk+1)*stepm;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+       dateintsum=0;
-           if(jl==0){
+       k2cpt=0;
-             dh[mi][i]=jk;
+       for (i=1; i<=imx; i++) {
-             bh[mi][i]=0;
+         bool=1;
-           }else{ /* We want a negative bias in order to only have interpolation ie
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-                   * at the price of an extra matrix product in likelihood */
+           for (z1=1; z1<=cptcoveff; z1++)
-             dh[mi][i]=jk+1;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-             bh[mi][i]=ju;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-           }
+               bool=0;
-         }else{
+               /* 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(jl <= -ju){
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-             dh[mi][i]=jk;
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-             bh[mi][i]=jl;       /* bias is positive if real duration
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-                                  * is higher than the multiple of stepm and negative otherwise.
+             }
-                                  */
+         }
-           }
-           else{
+         if (bool==1){
-             dh[mi][i]=jk+1;
+           for(m=firstpass; m<=lastpass; m++){
-             bh[mi][i]=ju;
+             k2=anint[m][i]+(mint[m][i]/12.);
-           }
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-           if(dh[mi][i]==0){
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-             dh[mi][i]=1; /* At least one step */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-             bh[mi][i]=ju; /* At least one step */
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+               if (m<lastpass) {
-           }
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-         } /* end if mle */
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-       }
+               }
-     } /* end wave */
-   }
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-   jmean=sum/k;
+                 dateintsum=dateintsum+k2;
-   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);
+                 k2cpt++;
-   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);
+               }
-  }
+               /*}*/
+           }
- /*********** Tricode ****************************/
+         }
- void tricode(int *Tvar, int **nbcode, int imx)
+       } /* end i */
- {
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+       pstamp(ficresp);
-   int cptcode=0;
+       if  (cptcovn>0) {
-   cptcoveff=0;
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+         fprintf(ficresp, "**********\n#");
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+         fprintf(ficlog, "**********\n#");
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+       }
-                                modality*/
+       for(i=1; i<=nlstate;i++)
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       Ndum[ij]++; /*store the modality */
+       fprintf(ficresp, "\n");
-       /*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=iagemin; i <= iagemax+3; i++){
-                                        Tvar[j]. If V=sex and male is 0 and
+         if(i==iagemax+3){
-                                        female is 1, then  cptcode=1.*/
+           fprintf(ficlog,"Total");
-     }
+         }else{
+           if(first==1){
-     for (i=0; i<=cptcode; i++) {
+             first=0;
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+             printf("See log file for details...\n");
-     }
+           }
+           fprintf(ficlog,"Age %d", i);
-     ij=1;
+         }
-     for (i=1; i<=ncodemax[j]; i++) {
+         for(jk=1; jk <=nlstate ; jk++){
-       for (k=0; k<= maxncov; k++) {
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-         if (Ndum[k] != 0) {
+             pp[jk] += freq[jk][m][i];
-           nbcode[Tvar[j]][ij]=k;
+         }
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-           ij++;
+             pos += freq[jk][m][i];
-         }
+           if(pp[jk]>=1.e-10){
-         if (ij > ncodemax[j]) break;
+             if(first==1){
-       }
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-     }
+             }
-   }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-  for (i=1; i<=ncovmodel-2; i++) {
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-    /* 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];
+         }
-    Ndum[ij]++;
-  }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-  ij=1;
+             pp[jk] += freq[jk][m][i];
-  for (i=1; i<= maxncov; i++) {
+         }
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-      Tvaraff[ij]=i; /*For printing */
+           pos += pp[jk];
-      ij++;
+           posprop += prop[jk][i];
-    }
+         }
-  }
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5){
-  cptcoveff=ij-1; /*Number of simple covariates*/
+             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);
- /*********** Health Expectancies ****************/
+           }else{
+             if(first==1)
- 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(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- {
+           }
-   /* Health expectancies, no variances */
+           if( i <= iagemax){
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+             if(pos>=1.e-5){
-   double age, agelim, hf;
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   double ***p3mat;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   double eip;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
-   pstamp(ficreseij);
+             else
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-   fprintf(ficreseij,"# Age");
+           }
-   for(i=1; i<=nlstate;i++){
+         }
-     for(j=1; j<=nlstate;j++){
-       fprintf(ficreseij," e%1d%1d ",i,j);
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-     }
+           for(m=-1; m <=nlstate+ndeath; m++)
-     fprintf(ficreseij," e%1d. ",i);
+             if(freq[jk][m][i] !=0 ) {
-   }
+             if(first==1)
-   fprintf(ficreseij,"\n");
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
-   if(estepm < stepm){
+         if(i <= iagemax)
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+           fprintf(ficresp,"\n");
-   }
+         if(first==1)
-   else  hstepm=estepm;
+           printf("Others in log...\n");
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+         fprintf(ficlog,"\n");
-    * This is mainly to measure the difference between two models: for example
+       }
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+       /*}*/
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   }
-    * progression in between and thus overestimating or underestimating according
+   dateintmean=dateintsum/k2cpt;
-    * 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
+   fclose(ficresp);
-    * to compare the new estimate of Life expectancy with the same linear
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-    * hypothesis. A more precise result, taking into account a more precise
+   free_vector(pp,1,nlstate);
-    * curvature will be obtained if estepm is as small as stepm. */
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of Freq */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+ }
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
+ /************ Prevalence ********************/
-      nstepm is the number of stepm from age to agelin.
+ 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)
-      Look at hpijx to understand the reason of that which relies in memory size
+ {
-      and note for a fixed period like estepm months */
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-      survival function given by stepm (the optimization length). Unfortunately it
+      We still use firstpass and lastpass as another selection.
-      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.
+   int i, m, jk, j1, bool, z1,j;
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   double **prop;
+   double posprop;
-   agelim=AGESUP;
+   double  y2; /* in fractional years */
-   /* If stepm=6 months */
+   int iagemin, iagemax;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+   int first; /** to stop verbosity which is redirected to log file */
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   iagemin= (int) agemin;
- /* nhstepm age range expressed in number of stepm */
+   iagemax= (int) agemax;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /*pp=vector(1,nlstate);*/
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   /* if (stepm >= YEARM) hstepm=1;*/
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   j1=0;
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /*j=cptcoveff;*/
-   for (age=bage; age<=fage; age ++){
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   first=1;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       j1++;*/
-     printf("%d|",(int)age);fflush(stdout);
+       for (i=1; i<=nlstate; i++)
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+         for(m=iagemin; m <= iagemax+3; m++)
+           prop[i][m]=0.0;
-     /* Computing expectancies */
+       for (i=1; i<=imx; i++) { /* Each individual */
-     for(i=1; i<=nlstate;i++)
+         bool=1;
-       for(j=1; j<=nlstate;j++)
+         if  (cptcovn>0) {
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           for (z1=1; z1<=cptcoveff; z1++)
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               bool=0;
-           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         }
+         if (bool==1) {
-         }
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-     fprintf(ficreseij,"%3.0f",age );
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-     for(i=1; i<=nlstate;i++){
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-       eip=0;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-       for(j=1; j<=nlstate;j++){
+               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);
-         eip +=eij[i][j][(int)age];
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-       }
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-       fprintf(ficreseij,"%9.4f", eip );
+                 prop[s[m][i]][iagemax+3] += weight[i];
-     }
+               }
-     fprintf(ficreseij,"\n");
+             }
+           } /* end selection of waves */
-   }
+         }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-   printf("\n");
+       for(i=iagemin; i <= iagemax+3; i++){
-   fprintf(ficlog,"\n");
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+           posprop += prop[jk][i];
- }
+         }
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <=  iagemax){
- {
+             if(posprop>=1.e-5){
-   /* Covariances of health expectancies eij and of total life expectancies according
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-    to initial status i, ei. .
+             } else{
-   */
+               if(first==1){
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+                 first=0;
-   double age, agelim, hf;
+                 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]);
-   double ***p3matp, ***p3matm, ***varhe;
+               }
-   double **dnewm,**doldm;
+             }
-   double *xp, *xm;
+           }
-   double **gp, **gm;
+         }/* end jk */
-   double ***gradg, ***trgradg;
+       }/* end i */
-   int theta;
+     /*} *//* end i1 */
+   } /* end j1 */
-   double eip, vip;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   /*free_vector(pp,1,nlstate);*/
-   xp=vector(1,npar);
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   xm=vector(1,npar);
+ }  /* End of prevalence */
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+ /************* Waves Concatenation ***************/
-   pstamp(ficresstdeij);
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+ {
-   fprintf(ficresstdeij,"# Age");
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   for(i=1; i<=nlstate;i++){
+      Death is a valid wave (if date is known).
-     for(j=1; j<=nlstate;j++)
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-     fprintf(ficresstdeij," e%1d. ",i);
+      and mw[mi+1][i]. dh depends on stepm.
-   }
+      */
-   fprintf(ficresstdeij,"\n");
+   int i, mi, m;
-   pstamp(ficrescveij);
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+      double sum=0., jmean=0.;*/
-   fprintf(ficrescveij,"# Age");
+   int first;
-   for(i=1; i<=nlstate;i++)
+   int j, k=0,jk, ju, jl;
-     for(j=1; j<=nlstate;j++){
+   double sum=0.;
-       cptj= (j-1)*nlstate+i;
+   first=0;
-       for(i2=1; i2<=nlstate;i2++)
+   jmin=100000;
-         for(j2=1; j2<=nlstate;j2++){
+   jmax=-1;
-           cptj2= (j2-1)*nlstate+i2;
+   jmean=0.;
-           if(cptj2 <= cptj)
+   for(i=1; i<=imx; i++){
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+     mi=0;
-         }
+     m=firstpass;
-     }
+     while(s[m][i] <= nlstate){
-   fprintf(ficrescveij,"\n");
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+         mw[++mi][i]=m;
-   if(estepm < stepm){
+       if(m >=lastpass)
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         break;
-   }
+       else
-   else  hstepm=estepm;
+         m++;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     }/* end while */
-    * This is mainly to measure the difference between two models: for example
+     if (s[m][i] > nlstate){
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+       mi++;     /* Death is another wave */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       /* if(mi==0)  never been interviewed correctly before death */
-    * progression in between and thus overestimating or underestimating according
+          /* Only death is a correct wave */
-    * to the curvature of the survival function. If, for the same date, we
+       mw[mi][i]=m;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+     }
-    * to compare the new estimate of Life expectancy with the same linear
-    * hypothesis. A more precise result, taking into account a more precise
+     wav[i]=mi;
-    * curvature will be obtained if estepm is as small as stepm. */
+     if(mi==0){
+       nbwarn++;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+       if(first==0){
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-      nhstepm is the number of hstepm from age to agelim
+         first=1;
-      nstepm is the number of stepm from age to agelin.
+       }
-      Look at hpijx to understand the reason of that which relies in memory size
+       if(first==1){
-      and note for a fixed period like estepm months */
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-   /* 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
+     } /* end mi==0 */
-      means that if the survival funtion is printed only each two years of age and if
+   } /* End individuals */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
+   for(i=1; i<=imx; i++){
-   */
+     for(mi=1; mi<wav[i];mi++){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       if (stepm <=0)
+         dh[mi][i]=1;
-   /* If stepm=6 months */
+       else{
-   /* nhstepm age range expressed in number of stepm */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-   agelim=AGESUP;
+           if (agedc[i] < 2*AGESUP) {
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   /* if (stepm >= YEARM) hstepm=1;*/
+             else if(j<0){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+               nberr++;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               j=1; /* Temporary Dangerous patch */
-   p3matm=ma3x(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);
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+               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]);
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+             }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+             k=k+1;
+             if (j >= jmax){
-   for (age=bage; age<=fage; age ++){
+               jmax=j;
+               ijmax=i;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+             }
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+             if (j <= jmin){
+               jmin=j;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+               ijmin=i;
+             }
-     /* Computing  Variances of health expectancies */
+             sum=sum+j;
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-        decrease memory allocation */
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-     for(theta=1; theta <=npar; theta++){
+           }
-       for(i=1; i<=npar; i++){
+         }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         else{
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-       }
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+           k=k+1;
+           if (j >= jmax) {
-       for(j=1; j<= nlstate; j++){
+             jmax=j;
-         for(i=1; i<=nlstate; i++){
+             ijmax=i;
-           for(h=0; h<=nhstepm-1; h++){
+           }
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+           else if (j <= jmin){
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+             jmin=j;
-           }
+             ijmin=i;
-         }
+           }
-       }
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+           if(j<0){
-         for(h=0; h<=nhstepm-1; h++){
+             nberr++;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         }
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-     }/* End theta */
+           }
+           sum=sum+j;
+         }
-     for(h=0; h<=nhstepm-1; h++)
+         jk= j/stepm;
-       for(j=1; j<=nlstate*nlstate;j++)
+         jl= j -jk*stepm;
-         for(theta=1; theta <=npar; theta++)
+         ju= j -(jk+1)*stepm;
-           trgradg[h][j][theta]=gradg[h][theta][j];
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+           if(jl==0){
+             dh[mi][i]=jk;
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+             bh[mi][i]=0;
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+           }else{ /* We want a negative bias in order to only have interpolation ie
-         varhe[ij][ji][(int)age] =0.;
+                   * to avoid the price of an extra matrix product in likelihood */
+             dh[mi][i]=jk+1;
-      printf("%d|",(int)age);fflush(stdout);
+             bh[mi][i]=ju;
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           }
-      for(h=0;h<=nhstepm-1;h++){
+         }else{
-       for(k=0;k<=nhstepm-1;k++){
+           if(jl <= -ju){
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+             dh[mi][i]=jk;
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+                                  * is higher than the multiple of stepm and negative otherwise.
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+                                  */
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+           }
-       }
+           else{
-     }
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
-     /* Computing expectancies */
+           }
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+           if(dh[mi][i]==0){
-     for(i=1; i<=nlstate;i++)
+             dh[mi][i]=1; /* At least one step */
-       for(j=1; j<=nlstate;j++)
+             bh[mi][i]=ju; /* At least one step */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+             /*  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);*/
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+           }
+         } /* end if mle */
-           /* 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]);*/
+       }
+     } /* end wave */
-         }
+   }
+   jmean=sum/k;
-     fprintf(ficresstdeij,"%3.0f",age );
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-     for(i=1; i<=nlstate;i++){
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-       eip=0.;
+  }
-       vip=0.;
-       for(j=1; j<=nlstate;j++){
+ /*********** Tricode ****************************/
-         eip += eij[i][j][(int)age];
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-         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];
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-       }
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-     }
+    * nbcode[Tvar[j]][1]=
-     fprintf(ficresstdeij,"\n");
+   */
-     fprintf(ficrescveij,"%3.0f",age );
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-     for(i=1; i<=nlstate;i++)
+   int modmaxcovj=0; /* Modality max of covariates j */
-       for(j=1; j<=nlstate;j++){
+   int cptcode=0; /* Modality max of covariates j */
-         cptj= (j-1)*nlstate+i;
+   int modmincovj=0; /* Modality min of covariates j */
-         for(i2=1; i2<=nlstate;i2++)
-           for(j2=1; j2<=nlstate;j2++){
-             cptj2= (j2-1)*nlstate+i2;
+   cptcoveff=0;
-             if(cptj2 <= cptj)
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-           }
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-       }
-     fprintf(ficrescveij,"\n");
+   /* Loop on covariates without age and products */
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-   }
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+                                modality of this covariate Vj*/
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+                                     * If product of Vn*Vm, still boolean *:
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   printf("\n");
+                                       modality of the nth covariate of individual i. */
-   fprintf(ficlog,"\n");
+       if (ij > modmaxcovj)
+         modmaxcovj=ij;
-   free_vector(xm,1,npar);
+       else if (ij < modmincovj)
-   free_vector(xp,1,npar);
+         modmincovj=ij;
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+       if ((ij < -1) && (ij > NCOVMAX)){
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+         exit(1);
- }
+       }else
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
- /************ Variance ******************/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
- 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[])
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
- {
+       /* getting the maximum value of the modality of the covariate
-   /* Variance of health expectancies */
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+          female is 1, then modmaxcovj=1.*/
-   /* double **newm;*/
+     }
-   double **dnewm,**doldm;
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   double **dnewmp,**doldmp;
+     cptcode=modmaxcovj;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   int k, cptcode;
+    /*for (i=0; i<=cptcode; i++) {*/
-   double *xp;
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-   double **gp, **gm;  /* for var eij */
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-   double ***gradg, ***trgradg; /*for var eij */
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-   double **gradgp, **trgradgp; /* for var p point j */
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-   double *gpp, *gmp; /* for var p point j */
+       }
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   double ***p3mat;
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   double age,agelim, hf;
+     } /* Ndum[-1] number of undefined modalities */
-   double ***mobaverage;
-   int theta;
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-   char digit[4];
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-   char digitp[25];
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+        modmincovj=3; modmaxcovj = 7;
-   char fileresprobmorprev[FILENAMELENGTH];
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-   if(popbased==1){
+        variables V1_1 and V1_2.
-     if(mobilav!=0)
+        nbcode[Tvar[j]][ij]=k;
-       strcpy(digitp,"-populbased-mobilav-");
+        nbcode[Tvar[j]][1]=0;
-     else strcpy(digitp,"-populbased-nomobil-");
+        nbcode[Tvar[j]][2]=1;
-   }
+        nbcode[Tvar[j]][3]=2;
-   else
+     */
-     strcpy(digitp,"-stablbased-");
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   if (mobilav!=0) {
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         /*recode from 0 */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                                      k is a modality. If we have model=V1+V1*sex
-     }
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-   }
+           ij++;
+         }
-   strcpy(fileresprobmorprev,"prmorprev");
+         if (ij > ncodemax[j]) break;
-   sprintf(digit,"%-d",ij);
+       }  /* end of loop on */
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+     } /* end of loop on modality */
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    /* 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 */
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    Ndum[ij]++;
+  }
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   pstamp(ficresprobmorprev);
+  ij=1;
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-     for(i=1; i<=nlstate;i++)
+      Tvaraff[ij]=i; /*For printing (unclear) */
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+      ij++;
-   }
+    }else
-   fprintf(ficresprobmorprev,"\n");
+        Tvaraff[ij]=0;
-   fprintf(ficgp,"\n# Routine varevsij");
+  }
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+  ij--;
-   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");
+  cptcoveff=ij; /*Number of total covariates*/
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- /*   } */
+ }
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+ /*********** Health Expectancies ****************/
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   else
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+ {
-   fprintf(ficresvij,"# Age");
+   /* Health expectancies, no variances */
-   for(i=1; i<=nlstate;i++)
+   int i, j, nhstepm, hstepm, h, nstepm;
-     for(j=1; j<=nlstate;j++)
+   int nhstepma, nstepma; /* Decreasing with age */
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   double age, agelim, hf;
-   fprintf(ficresvij,"\n");
+   double ***p3mat;
+   double eip;
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   pstamp(ficreseij);
-   doldm=matrix(1,nlstate,1,nlstate);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   fprintf(ficreseij,"# Age");
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++){
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+       fprintf(ficreseij," e%1d%1d ",i,j);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+     }
-   gmp=vector(nlstate+1,nlstate+ndeath);
+     fprintf(ficreseij," e%1d. ",i);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   }
+   fprintf(ficreseij,"\n");
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+   if(estepm < stepm){
-   else  hstepm=estepm;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   }
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   else  hstepm=estepm;
-      nhstepm is the number of hstepm from age to agelim
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-      nstepm is the number of stepm from age to agelin.
+    * This is mainly to measure the difference between two models: for example
-      Look at hpijx to understand the reason of that which relies in memory size
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-      and note for a fixed period like k years */
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+    * progression in between and thus overestimating or underestimating according
-      survival function given by stepm (the optimization length). Unfortunately it
+    * to the curvature of the survival function. If, for the same date, we
-      means that if the survival funtion is printed every two years of age and if
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+    * to compare the new estimate of Life expectancy with the same linear
-      results. So we changed our mind and took the option of the best precision.
+    * hypothesis. A more precise result, taking into account a more precise
-   */
+    * curvature will be obtained if estepm is as small as stepm. */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+      nhstepm is the number of hstepm from age to agelim
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      nstepm is the number of stepm from age to agelin.
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      Look at hpijx to understand the reason of that which relies in memory size
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+      and note for a fixed period like estepm months */
-     gp=matrix(0,nhstepm,1,nlstate);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     gm=matrix(0,nhstepm,1,nlstate);
+      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
-     for(theta=1; theta <=npar; theta++){
+      results. So we changed our mind and took the option of the best precision.
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   agelim=AGESUP;
-       prevalim(prlim,nlstate,xp,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 ++){
-       for(j=1; j<= nlstate; j++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-         for(h=0; h<=nhstepm; h++){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+     /* if (stepm >= YEARM) hstepm=1;*/
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-         }
-       }
+     /* If stepm=6 months */
-       /* This for computing probability of death (h=1 means
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-          computed over hstepm matrices product = hstepm*stepm months)
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-          as a weighted average of prlim.
-       */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+     printf("%d|",(int)age);fflush(stdout);
-       /* end probability of death */
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+     /* Computing expectancies */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     for(i=1; i<=nlstate;i++)
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       for(j=1; j<=nlstate;j++)
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       if (popbased==1) {
-         if(mobilav ==0){
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+         }
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+     fprintf(ficreseij,"%3.0f",age );
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     for(i=1; i<=nlstate;i++){
-         }
+       eip=0;
-       }
+       for(j=1; j<=nlstate;j++){
+         eip +=eij[i][j][(int)age];
-       for(j=1; j<= nlstate; j++){
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-         for(h=0; h<=nhstepm; h++){
+       }
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+       fprintf(ficreseij,"%9.4f", eip );
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+     }
-         }
+     fprintf(ficreseij,"\n");
-       }
-       /* This for computing probability of death (h=1 means
+   }
-          computed over hstepm matrices product = hstepm*stepm months)
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-          as a weighted average of prlim.
+   printf("\n");
-       */
+   fprintf(ficlog,"\n");
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+ }
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+ 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[] )
-       /* end probability of death */
+ {
-       for(j=1; j<= nlstate; j++) /* vareij */
+   /* Covariances of health expectancies eij and of total life expectancies according
-         for(h=0; h<=nhstepm; h++){
+    to initial status i, ei. .
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   */
-         }
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   int nhstepma, nstepma; /* Decreasing with age */
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   double age, agelim, hf;
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   double ***p3matp, ***p3matm, ***varhe;
-       }
+   double **dnewm,**doldm;
+   double *xp, *xm;
-     } /* End theta */
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   int theta;
-     for(h=0; h<=nhstepm; h++) /* veij */
+   double eip, vip;
-       for(j=1; j<=nlstate;j++)
-         for(theta=1; theta <=npar; theta++)
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   xp=vector(1,npar);
+   xm=vector(1,npar);
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-       for(theta=1; theta <=npar; theta++)
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-         trgradgp[j][theta]=gradgp[theta][j];
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   fprintf(ficresstdeij,"# Age");
-     for(i=1;i<=nlstate;i++)
+   for(i=1; i<=nlstate;i++){
-       for(j=1;j<=nlstate;j++)
+     for(j=1; j<=nlstate;j++)
-         vareij[i][j][(int)age] =0.;
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     fprintf(ficresstdeij," e%1d. ",i);
-     for(h=0;h<=nhstepm;h++){
+   }
-       for(k=0;k<=nhstepm;k++){
+   fprintf(ficresstdeij,"\n");
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+   pstamp(ficrescveij);
-         for(i=1;i<=nlstate;i++)
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-           for(j=1;j<=nlstate;j++)
+   fprintf(ficrescveij,"# Age");
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+   for(i=1; i<=nlstate;i++)
-       }
+     for(j=1; j<=nlstate;j++){
-     }
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
-     /* pptj */
+         for(j2=1; j2<=nlstate;j2++){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+           cptj2= (j2-1)*nlstate+i2;
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+           if(cptj2 <= cptj)
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         }
-         varppt[j][i]=doldmp[j][i];
+     }
-     /* end ppptj */
+   fprintf(ficrescveij,"\n");
-     /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   if(estepm < stepm){
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-     if (popbased==1) {
+   else  hstepm=estepm;
-       if(mobilav ==0){
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-         for(i=1; i<=nlstate;i++)
+    * This is mainly to measure the difference between two models: for example
-           prlim[i][i]=probs[(int)age][i][ij];
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-       }else{ /* mobilav */
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-         for(i=1; i<=nlstate;i++)
+    * progression in between and thus overestimating or underestimating according
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+    * to the curvature of the survival function. If, for the same date, we
-       }
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-     }
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
-     /* This for computing probability of death (h=1 means
+    * curvature will be obtained if estepm is as small as stepm. */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+      nhstepm is the number of hstepm from age to agelim
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+      nstepm is the number of stepm from age to agelin.
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+      Look at hpijx to understand the reason of that which relies in memory size
-     }
+      and note for a fixed period like estepm months */
-     /* end probability of death */
+   /* 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
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      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
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+      results. So we changed our mind and took the option of the best precision.
-       for(i=1; i<=nlstate;i++){
+   */
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       }
-     }
+   /* If stepm=6 months */
-     fprintf(ficresprobmorprev,"\n");
+   /* nhstepm age range expressed in number of stepm */
+   agelim=AGESUP;
-     fprintf(ficresvij,"%.0f ",age );
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     for(i=1; i<=nlstate;i++)
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(j=1; j<=nlstate;j++){
+   /* if (stepm >= YEARM) hstepm=1;*/
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       }
-     fprintf(ficresvij,"\n");
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_matrix(gp,0,nhstepm,1,nlstate);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+   for (age=bage; age<=fage; age ++){
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+     /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   /* 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)\";");
+     /* If stepm=6 months */
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   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));
+     /* Computing  Variances of health expectancies */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   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);
+        decrease memory allocation */
-   /*  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);
+     for(theta=1; theta <=npar; theta++){
- */
+       for(i=1; i<=npar; i++){
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+       }
-   free_vector(xp,1,npar);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       for(j=1; j<= nlstate; j++){
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+         for(i=1; i<=nlstate; i++){
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+           for(h=0; h<=nhstepm-1; h++){
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   fclose(ficresprobmorprev);
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   fflush(ficgp);
+           }
-   fflush(fichtm);
+         }
- }  /* end varevsij */
+       }
- /************ Variance of prevlim ******************/
+       for(ij=1; ij<= nlstate*nlstate; ij++)
- 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[])
+         for(h=0; h<=nhstepm-1; h++){
- {
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   /* Variance of prevalence limit */
+         }
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+     }/* End theta */
-   double **newm;
-   double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm;
+     for(h=0; h<=nhstepm-1; h++)
-   int k, cptcode;
+       for(j=1; j<=nlstate*nlstate;j++)
-   double *xp;
+         for(theta=1; theta <=npar; theta++)
-   double *gp, *gm;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   double **gradg, **trgradg;
-   double age,agelim;
-   int theta;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   pstamp(ficresvpl);
+         varhe[ij][ji][(int)age] =0.;
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+      printf("%d|",(int)age);fflush(stdout);
-   for(i=1; i<=nlstate;i++)
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       fprintf(ficresvpl," %1d-%1d",i,i);
+      for(h=0;h<=nhstepm-1;h++){
-   fprintf(ficresvpl,"\n");
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-   xp=vector(1,npar);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   dnewm=matrix(1,nlstate,1,npar);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   doldm=matrix(1,nlstate,1,nlstate);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   hstepm=1*YEARM; /* Every year of age */
+       }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     }
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     /* Computing expectancies */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-     if (stepm >= YEARM) hstepm=1;
+     for(i=1; i<=nlstate;i++)
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       for(j=1; j<=nlstate;j++)
-     gradg=matrix(1,npar,1,nlstate);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-     gp=vector(1,nlstate);
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-     gm=vector(1,nlstate);
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+         }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       }
+     fprintf(ficresstdeij,"%3.0f",age );
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     for(i=1; i<=nlstate;i++){
-       for(i=1;i<=nlstate;i++)
+       eip=0.;
-         gp[i] = prlim[i][i];
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
-       for(i=1; i<=npar; i++) /* Computes gradient */
+         eip += eij[i][j][(int)age];
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-       for(i=1;i<=nlstate;i++)
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-         gm[i] = prlim[i][i];
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-       for(i=1;i<=nlstate;i++)
+     }
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+     fprintf(ficresstdeij,"\n");
-     } /* End theta */
+     fprintf(ficrescveij,"%3.0f",age );
-     trgradg =matrix(1,nlstate,1,npar);
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-     for(j=1; j<=nlstate;j++)
+         cptj= (j-1)*nlstate+i;
-       for(theta=1; theta <=npar; theta++)
+         for(i2=1; i2<=nlstate;i2++)
-         trgradg[j][theta]=gradg[theta][j];
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
-     for(i=1;i<=nlstate;i++)
+             if(cptj2 <= cptj)
-       varpl[i][(int)age] =0.;
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-     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++)
+     fprintf(ficrescveij,"\n");
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   }
-     fprintf(ficresvpl,"%.0f ",age );
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     for(i=1; i<=nlstate;i++)
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     fprintf(ficresvpl,"\n");
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_vector(gp,1,nlstate);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_vector(gm,1,nlstate);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_matrix(gradg,1,npar,1,nlstate);
+   printf("\n");
-     free_matrix(trgradg,1,nlstate,1,npar);
+   fprintf(ficlog,"\n");
-   } /* End age */
+   free_vector(xm,1,npar);
    free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
- /************ Variance of one-step probabilities  ******************/
+ /************ Variance ******************/
- 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[])
+ 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[])
  {
-   int i, j=0,  i1, k1, l1, t, tj;
+   /* Variance of health expectancies */
-   int k2, l2, j1,  z1;
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   int k=0,l, cptcode;
+   /* double **newm;*/
-   int first=1, first1;
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+   int movingaverage();
-   double *xp;
+   double **dnewm,**doldm;
-   double *gp, *gm;
+   double **dnewmp,**doldmp;
-   double **gradg, **trgradg;
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   double **mu;
+   int k;
-   double age,agelim, cov[NCOVMAX];
+   double *xp;
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   double **gp, **gm;  /* for var eij */
-   int theta;
+   double ***gradg, ***trgradg; /*for var eij */
-   char fileresprob[FILENAMELENGTH];
+   double **gradgp, **trgradgp; /* for var p point j */
-   char fileresprobcov[FILENAMELENGTH];
+   double *gpp, *gmp; /* for var p point j */
-   char fileresprobcor[FILENAMELENGTH];
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   double ***p3mat;
-   double ***varpij;
+   double age,agelim, hf;
+   double ***mobaverage;
-   strcpy(fileresprob,"prob");
+   int theta;
-   strcat(fileresprob,fileres);
+   char digit[4];
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   char digitp[25];
-     printf("Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   char fileresprobmorprev[FILENAMELENGTH];
-   }
-   strcpy(fileresprobcov,"probcov");
+   if(popbased==1){
-   strcat(fileresprobcov,fileres);
+     if(mobilav!=0)
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+       strcpy(digitp,"-populbased-mobilav-");
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+     else strcpy(digitp,"-populbased-nomobil-");
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
-   }
+   else
-   strcpy(fileresprobcor,"probcor");
+     strcpy(digitp,"-stablbased-");
-   strcat(fileresprobcor,fileres);
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   if (mobilav!=0) {
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   }
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+     }
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   }
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   strcpy(fileresprobmorprev,"prmorprev");
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   sprintf(digit,"%-d",ij);
-   pstamp(ficresprob);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   fprintf(ficresprob,"# Age");
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   pstamp(ficresprobcov);
+   strcat(fileresprobmorprev,fileres);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   fprintf(ficresprobcov,"# Age");
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   pstamp(ficresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   }
-   fprintf(ficresprobcor,"# Age");
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   for(i=1; i<=nlstate;i++)
+   pstamp(ficresprobmorprev);
-     for(j=1; j<=(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);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-     }
+     for(i=1; i<=nlstate;i++)
-  /* fprintf(ficresprob,"\n");
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   fprintf(ficresprobcov,"\n");
+   }
-   fprintf(ficresprobcor,"\n");
+   fprintf(ficresprobmorprev,"\n");
-  */
+   fprintf(ficgp,"\n# Routine varevsij");
-  xp=vector(1,npar);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   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");
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+ /*   } */
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   first=1;
+   pstamp(ficresvij);
-   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   if(popbased==1)
-   fprintf(fichtm,"\n");
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+   else
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   fprintf(ficresvij,"# Age");
-   file %s<br>\n",optionfilehtmcov);
+   for(i=1; i<=nlstate;i++)
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+     for(j=1; j<=nlstate;j++)
- and drawn. It helps understanding how is the covariance between two incidences.\
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(ficresvij,"\n");
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   xp=vector(1,npar);
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+   dnewm=matrix(1,nlstate,1,npar);
- standard deviations wide on each axis. <br>\
+   doldm=matrix(1,nlstate,1,nlstate);
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   cov[1]=1;
+   gpp=vector(nlstate+1,nlstate+ndeath);
-   tj=cptcoveff;
+   gmp=vector(nlstate+1,nlstate+ndeath);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   j1=0;
-   for(t=1; t<=tj;t++){
+   if(estepm < stepm){
-     for(i1=1; i1<=ncodemax[t];i1++){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       j1++;
+   }
-       if  (cptcovn>0) {
+   else  hstepm=estepm;
-         fprintf(ficresprob, "\n#********** Variable ");
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-         fprintf(ficresprob, "**********\n#\n");
+      nhstepm is the number of hstepm from age to agelim
-         fprintf(ficresprobcov, "\n#********** Variable ");
+      nstepm is the number of stepm from age to agelin.
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-         fprintf(ficresprobcov, "**********\n#\n");
+   /* 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
-         fprintf(ficgp, "\n#********** Variable ");
+      means that if the survival funtion is printed every two years of age and if
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         fprintf(ficgp, "**********\n#\n");
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+   agelim = AGESUP;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+     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 */
-         fprintf(ficresprobcor, "\n#********** Variable ");
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         fprintf(ficresprobcor, "**********\n#");
+     gp=matrix(0,nhstepm,1,nlstate);
-       }
+     gm=matrix(0,nhstepm,1,nlstate);
-       for (age=bage; age<=fage; age ++){
-         cov[2]=age;
+     for(theta=1; theta <=npar; theta++){
-         for (k=1; k<=cptcovn;k++) {
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         }
+       }
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         for (k=1; k<=cptcovprod;k++)
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       if (popbased==1) {
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+         if(mobilav ==0){
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+           for(i=1; i<=nlstate;i++)
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+             prlim[i][i]=probs[(int)age][i][ij];
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
-         for(theta=1; theta <=npar; theta++){
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-           for(i=1; i<=npar; i++)
+         }
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+       }
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+       for(j=1; j<= nlstate; j++){
+         for(h=0; h<=nhstepm; h++){
-           k=0;
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-           for(i=1; i<= (nlstate); i++){
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-             for(j=1; j<=(nlstate+ndeath);j++){
+         }
-               k=k+1;
+       }
-               gp[k]=pmmij[i][j];
+       /* This for computing probability of death (h=1 means
-             }
+          computed over hstepm matrices product = hstepm*stepm months)
-           }
+          as a weighted average of prlim.
+       */
-           for(i=1; i<=npar; i++)
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+       }
-           k=0;
+       /* end probability of death */
-           for(i=1; i<=(nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-               k=k+1;
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-               gm[k]=pmmij[i][j];
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-             }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           }
+       if (popbased==1) {
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+         if(mobilav ==0){
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+           for(i=1; i<=nlstate;i++)
-         }
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+           for(i=1; i<=nlstate;i++)
-           for(theta=1; theta <=npar; theta++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-             trgradg[j][theta]=gradg[theta][j];
+         }
+       }
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+         for(h=0; h<=nhstepm; h++){
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+         }
+       }
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-         k=0;
+          as a weighted average of prlim.
-         for(i=1; i<=(nlstate); i++){
+       */
-           for(j=1; j<=(nlstate+ndeath);j++){
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-             k=k+1;
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-             mu[k][(int) age]=pmmij[i][j];
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-           }
+       }
-         }
+       /* end probability of death */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+       for(j=1; j<= nlstate; j++) /* vareij */
-             varpij[i][j][(int)age] = doldm[i][j];
+         for(h=0; h<=nhstepm; h++){
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         /*printf("\n%d ",(int)age);
+         }
-           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]));
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-           }*/
+       }
-         fprintf(ficresprob,"\n%d ",(int)age);
+     } /* End theta */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+     for(h=0; h<=nhstepm; h++) /* veij */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+       for(j=1; j<=nlstate;j++)
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         for(theta=1; theta <=npar; theta++)
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-         i=0;
+       for(theta=1; theta <=npar; theta++)
-         for (k=1; k<=(nlstate);k++){
+         trgradgp[j][theta]=gradgp[theta][j];
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     for(i=1;i<=nlstate;i++)
-             for (j=1; j<=i;j++){
+       for(j=1;j<=nlstate;j++)
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+         vareij[i][j][(int)age] =0.;
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
+     for(h=0;h<=nhstepm;h++){
-           }
+       for(k=0;k<=nhstepm;k++){
-         }/* end of loop for state */
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-       } /* end of loop for age */
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+         for(i=1;i<=nlstate;i++)
-       /* Confidence intervalle of pij  */
+           for(j=1;j<=nlstate;j++)
-       /*
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-         fprintf(ficgp,"\nset noparametric;unset label");
+       }
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     }
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         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);
+     /* pptj */
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-       */
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         varppt[j][i]=doldmp[j][i];
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     /* end ppptj */
-       first1=1;
+     /*  x centered again */
-       for (k2=1; k2<=(nlstate);k2++){
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+     prevalim(prlim,nlstate,x,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;
+     /* This for computing probability of death (h=1 means
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+        as a weighted average of prlim.
-                   c12=cv12/sqrt(v1*v2);
+     */
-                   /* Computing eigen value of matrix of covariance */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-                   /* Eigen vectors */
+     }
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     /* end probability of death */
-                   /*v21=sqrt(1.-v11*v11); *//* error */
-                   v21=(lc1-v1)/cv12*v11;
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-                   v12=-v21;
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-                   v22=v11;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-                   tnalp=v21/v11;
+       for(i=1; i<=nlstate;i++){
-                   if(first1==1){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-                     first1=0;
+       }
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+     }
-                   }
+     fprintf(ficresprobmorprev,"\n");
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-                   /*printf(fignu*/
+     fprintf(ficresvij,"%.0f ",age );
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+     for(i=1; i<=nlstate;i++)
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+       for(j=1; j<=nlstate;j++){
-                   if(first==1){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-                     first=0;
+       }
-                     fprintf(ficgp,"\nset parametric;unset label");
+     fprintf(ficresvij,"\n");
-                     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);
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   } /* End age */
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-                     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",\
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                   }else{
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                     first=0;
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-                     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",\
+   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);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   /*  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);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ */
-                   }/* if first */
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                 } /* age mod 5 */
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-               } /* end loop age */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_vector(xp,1,npar);
-               first=1;
+   free_matrix(doldm,1,nlstate,1,nlstate);
-             } /*l12 */
+   free_matrix(dnewm,1,nlstate,1,npar);
-           } /* k12 */
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         } /*l1 */
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-       }/* k1 */
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     } /* loop covariates */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   }
+   fclose(ficresprobmorprev);
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   fflush(ficgp);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   fflush(fichtm);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ }  /* end varevsij */
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_vector(xp,1,npar);
+ /************ Variance of prevlim ******************/
-   fclose(ficresprob);
+ 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[])
-   fclose(ficresprobcov);
+ {
-   fclose(ficresprobcor);
+   /* Variance of prevalence limit */
-   fflush(ficgp);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   fflush(fichtmcov);
- }
+   double **dnewm,**doldm;
+   int i, j, nhstepm, hstepm;
+   double *xp;
- /******************* Printing html file ***********/
+   double *gp, *gm;
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   double **gradg, **trgradg;
-                   int lastpass, int stepm, int weightopt, char model[],\
+   double age,agelim;
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   int theta;
-                   int popforecast, int estepm ,\
-                   double jprev1, double mprev1,double anprev1, \
+   pstamp(ficresvpl);
-                   double jprev2, double mprev2,double anprev2){
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   int jj1, k1, i1, cpt;
+   fprintf(ficresvpl,"# Age");
+   for(i=1; i<=nlstate;i++)
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+       fprintf(ficresvpl," %1d-%1d",i,i);
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   fprintf(ficresvpl,"\n");
- </ul>");
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   xp=vector(1,npar);
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+   dnewm=matrix(1,nlstate,1,npar);
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   doldm=matrix(1,nlstate,1,nlstate);
-    fprintf(fichtm,"\
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   hstepm=1*YEARM; /* Every year of age */
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-    fprintf(fichtm,"\
+   agelim = AGESUP;
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-    fprintf(fichtm,"\
+     if (stepm >= YEARM) hstepm=1;
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-    <a href=\"%s\">%s</a> <br>\n",
+     gradg=matrix(1,npar,1,nlstate);
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+     gp=vector(1,nlstate);
-    fprintf(fichtm,"\
+     gm=vector(1,nlstate);
-  - Population projections by age and states: \
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
-  m=cptcoveff;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       for(i=1;i<=nlstate;i++)
+         gp[i] = prlim[i][i];
-  jj1=0;
-  for(k1=1; k1<=m;k1++){
+       for(i=1; i<=npar; i++) /* Computes gradient */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-      jj1++;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-      if (cptcovn > 0) {
+       for(i=1;i<=nlstate;i++)
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         gm[i] = prlim[i][i];
-        for (cpt=1; cpt<=cptcoveff;cpt++)
-          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\">");
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-      }
+     } /* End theta */
-      /* Pij */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
+     trgradg =matrix(1,nlstate,1,npar);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-      /* Quasi-incidences */
+     for(j=1; j<=nlstate;j++)
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+       for(theta=1; theta <=npar; theta++)
-  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> \
+         trgradg[j][theta]=gradg[theta][j];
- <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 */
+     for(i=1;i<=nlstate;i++)
-        for(cpt=1; cpt<nlstate;cpt++){
+       varpl[i][(int)age] =0.;
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-        }
+     for(i=1;i<=nlstate;i++)
-      for(cpt=1; cpt<=nlstate;cpt++) {
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-         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(ficresvpl,"%.0f ",age );
-      }
+     for(i=1; i<=nlstate;i++)
-    } /* end i1 */
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-  }/* End k1 */
+     fprintf(ficresvpl,"\n");
-  fprintf(fichtm,"</ul>");
+     free_vector(gp,1,nlstate);
+     free_vector(gm,1,nlstate);
+     free_matrix(gradg,1,npar,1,nlstate);
-  fprintf(fichtm,"\
+     free_matrix(trgradg,1,nlstate,1,npar);
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   } /* End age */
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   free_vector(xp,1,npar);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   free_matrix(doldm,1,nlstate,1,npar);
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-  fprintf(fichtm,"\
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ }
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+ /************ Variance of one-step probabilities  ******************/
-  fprintf(fichtm,"\
+ 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[])
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ {
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   int i, j=0,  k1, l1, tj;
-  fprintf(fichtm,"\
+   int k2, l2, j1,  z1;
-  - 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): \
+   int k=0, l;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   int first=1, first1, first2;
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-  fprintf(fichtm,"\
+   double **dnewm,**doldm;
-  - (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): \
+   double *xp;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   double *gp, *gm;
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   double **gradg, **trgradg;
-  fprintf(fichtm,"\
+   double **mu;
-  - 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",
+   double age, cov[NCOVMAX+1];
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-  fprintf(fichtm,"\
+   int theta;
-  - 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",
+   char fileresprob[FILENAMELENGTH];
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   char fileresprobcov[FILENAMELENGTH];
-  fprintf(fichtm,"\
+   char fileresprobcor[FILENAMELENGTH];
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   double ***varpij;
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   strcpy(fileresprob,"prob");
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   strcat(fileresprob,fileres);
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+     printf("Problem with resultfile: %s\n", fileresprob);
- /*      <br>",fileres,fileres,fileres,fileres); */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
- /*  else  */
+   }
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+   strcpy(fileresprobcov,"probcov");
-  fflush(fichtm);
+   strcat(fileresprobcov,fileres);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-  m=cptcoveff;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   }
+   strcpy(fileresprobcor,"probcor");
-  jj1=0;
+   strcat(fileresprobcor,fileres);
-  for(k1=1; k1<=m;k1++){
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-      jj1++;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-      if (cptcovn > 0) {
+   }
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-      }
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   pstamp(ficresprob);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   fprintf(ficresprob,"# Age");
-      }
+   pstamp(ficresprobcov);
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- health expectancies in states (1) and (2): %s%d.png<br>\
+   fprintf(ficresprobcov,"# Age");
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+   pstamp(ficresprobcor);
-    } /* end i1 */
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-  }/* End k1 */
+   fprintf(ficresprobcor,"# Age");
-  fprintf(fichtm,"</ul>");
-  fflush(fichtm);
- }
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
- /******************* Gnuplot file **************/
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-   char dirfileres[132],optfileres[132];
+     }
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  /* fprintf(ficresprob,"\n");
-   int ng;
+   fprintf(ficresprobcov,"\n");
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+   fprintf(ficresprobcor,"\n");
- /*     printf("Problem with file %s",optionfilegnuplot); */
+  */
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   xp=vector(1,npar);
- /*   } */
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   /*#ifdef windows */
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-     /*#endif */
+   first=1;
-   m=pow(2,cptcoveff);
+   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   strcpy(dirfileres,optionfilefiname);
+   fprintf(fichtm,"\n");
-   strcpy(optfileres,"vpl");
-  /* 1eme*/
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-    for (k1=1; k1<= m ; k1 ++) {
+   file %s<br>\n",optionfilehtmcov);
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- set ylabel \"Probability\" \n\
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- set ter png small\n\
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
- set size 0.65,0.65\n\
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+ standard deviations wide on each axis. <br>\
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-      for (i=1; i<= nlstate ; i ++) {
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+   cov[1]=1;
-      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);
+   /* tj=cptcoveff; */
-      for (i=1; i<= nlstate ; i ++) {
+   tj = (int) pow(2,cptcoveff);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   j1=0;
-      }
+   for(j1=1; j1<=tj;j1++){
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-      for (i=1; i<= nlstate ; i ++) {
+     /*j1++;*/
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       if  (cptcovn>0) {
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprob, "\n#********** Variable ");
-      }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         fprintf(ficresprob, "**********\n#\n");
-    }
+         fprintf(ficresprobcov, "\n#********** Variable ");
-   }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   /*2 eme*/
+         fprintf(ficresprobcov, "**********\n#\n");
-   for (k1=1; k1<= m ; k1 ++) {
+         fprintf(ficgp, "\n#********** Variable ");
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+         fprintf(ficgp, "**********\n#\n");
-     for (i=1; i<= nlstate+1 ; i ++) {
-       k=2*i;
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       for (j=1; j<= nlstate+1 ; j ++) {
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprobcor, "\n#********** Variable ");
-       }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+         fprintf(ficresprobcor, "**********\n#");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+       }
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-       }
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-       fprintf(ficgp,"\" t\"\" w l 0,");
+       for (age=bage; age<=fage; age ++){
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         cov[2]=age;
-       for (j=1; j<= nlstate+1 ; j ++) {
+         for (k=1; k<=cptcovn;k++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                                          * 1  1 1 1 1
-       }
+                                                          * 2  2 1 1 1
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+                                                          * 3  1 2 1 1
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+                                                          */
-     }
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-   }
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-   /*3eme*/
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       /*       k=2+nlstate*(2*cpt-2); */
+         for(theta=1; theta <=npar; theta++){
-       k=2+(nlstate+1)*(cpt-1);
+           for(i=1; i<=npar; i++)
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       fprintf(ficgp,"set ter png small\n\
- set size 0.65,0.65\n\
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           k=0;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           for(i=1; i<= (nlstate); i++){
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+             for(j=1; j<=(nlstate+ndeath);j++){
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+               k=k+1;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+               gp[k]=pmmij[i][j];
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+             }
+           }
-       */
-       for (i=1; i< nlstate ; i ++) {
+           for(i=1; i<=npar; i++)
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-         /*      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);*/
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       }
+           k=0;
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+           for(i=1; i<=(nlstate); i++){
-     }
+             for(j=1; j<=(nlstate+ndeath);j++){
-   }
+               k=k+1;
+               gm[k]=pmmij[i][j];
-   /* CV preval stable (period) */
+             }
-   for (k1=1; k1<= m ; k1 ++) {
+           }
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
-       k=3;
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         }
- set ter png small\nset size 0.65,0.65\n\
- unset log y\n\
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+           for(theta=1; theta <=npar; theta++)
+             trgradg[j][theta]=gradg[theta][j];
-       for (i=1; i< nlstate ; i ++)
-         fprintf(ficgp,"+$%d",k+i+1);
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-       l=3+(nlstate+ndeath)*cpt;
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-       for (i=1; i< nlstate ; i ++) {
+         k=0;
-         l=3+(nlstate+ndeath)*cpt;
+         for(i=1; i<=(nlstate); i++){
-         fprintf(ficgp,"+$%d",l+i+1);
+           for(j=1; j<=(nlstate+ndeath);j++){
-       }
+             k=k+1;
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+             mu[k][(int) age]=pmmij[i][j];
-     }
+           }
-   }
+         }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-   /* proba elementaires */
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-   for(i=1,jk=1; i <=nlstate; i++){
+             varpij[i][j][(int)age] = doldm[i][j];
-     for(k=1; k <=(nlstate+ndeath); k++){
-       if (k != i) {
+         /*printf("\n%d ",(int)age);
-         for(j=1; j <=ncovmodel; j++){
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           jk++;
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficgp,"\n");
+           }*/
-         }
-       }
+         fprintf(ficresprob,"\n%d ",(int)age);
-     }
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-    }
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-      for(jk=1; jk <=m; jk++) {
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-        if (ng==2)
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-        else
+         }
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+         i=0;
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         for (k=1; k<=(nlstate);k++){
-        i=1;
+           for (l=1; l<=(nlstate+ndeath);l++){
-        for(k2=1; k2<=nlstate; k2++) {
+             i++;
-          k3=i;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-          for(k=1; k<=(nlstate+ndeath); k++) {
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-            if (k != k2){
+             for (j=1; j<=i;j++){
-              if(ng==2)
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-              else
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+             }
-              ij=1;
+           }
-              for(j=3; j <=ncovmodel; j++) {
+         }/* end of loop for state */
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       } /* end of loop for age */
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-                  ij++;
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-                }
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                else
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-              }
+       /* Confidence intervalle of pij  */
-              fprintf(ficgp,")/(1");
+       /*
+         fprintf(ficgp,"\nunset parametric;unset label");
-              for(k1=1; k1 <=nlstate; k1++){
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                ij=1;
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-                for(j=3; j <=ncovmodel; j++){
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-                    ij++;
+       */
-                  }
-                  else
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       first1=1;first2=2;
-                }
+       for (k2=1; k2<=(nlstate);k2++){
-                fprintf(ficgp,")");
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-              }
+           if(l2==k2) continue;
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+           j=(k2-1)*(nlstate+ndeath)+l2;
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+           for (k1=1; k1<=(nlstate);k1++){
-              i=i+ncovmodel;
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-            }
+               if(l1==k1) continue;
-          } /* end k */
+               i=(k1-1)*(nlstate+ndeath)+l1;
-        } /* end k2 */
+               if(i<=j) continue;
-      } /* end jk */
+               for (age=bage; age<=fage; age ++){
-    } /* end ng */
+                 if ((int)age %5==0){
-    fflush(ficgp);
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
- }  /* end gnuplot */
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
- /*************** Moving average **************/
+                   mu2=mu[j][(int) age]/stepm*YEARM;
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
-   int i, cpt, cptcod;
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   int modcovmax =1;
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   int mobilavrange, mob;
+                   if ((lc2 <0) || (lc1 <0) ){
-   double age;
+                     if(first2==1){
+                       first1=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                     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);
-                            a covariate has 2 modalities */
+                     }
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+                     /* lc2=fabs(lc2); */
-     if(mobilav==1) mobilavrange=5; /* default */
+                   }
-     else mobilavrange=mobilav;
-     for (age=bage; age<=fage; age++)
+                   /* Eigen vectors */
-       for (i=1; i<=nlstate;i++)
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                   v21=(lc1-v1)/cv12*v11;
-     /* We keep the original values on the extreme ages bage, fage and for
+                   v12=-v21;
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                   v22=v11;
-        we use a 5 terms etc. until the borders are no more concerned.
+                   tnalp=v21/v11;
-     */
+                   if(first1==1){
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                     first1=0;
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                     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<=nlstate;i++){
+                   }
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                   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);
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                   /*printf(fignu*/
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                   if(first==1){
-               }
+                     first=0;
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+                     fprintf(ficgp,"\nset parametric;unset label");
-           }
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-         }
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-       }/* end age */
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-     }/* end mob */
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-   }else return -1;
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-   return 0;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
- }/* End movingaverage */
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
- /************** Forecasting ******************/
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- 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){
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   /* proj1, year, month, day of starting projection
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-      agemin, agemax range of age
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-      anproj2 year of en of projection (same day and month as proj1).
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   */
+                   }else{
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+                     first=0;
-   int *popage;
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-   double agec; /* generic age */
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   double *popeffectif,*popcount;
+                     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",\
-   double ***p3mat;
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   double ***mobaverage;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   char fileresf[FILENAMELENGTH];
+                   }/* if first */
+                 } /* age mod 5 */
-   agelim=AGESUP;
+               } /* end loop age */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+               first=1;
-   strcpy(fileresf,"f");
+             } /*l12 */
-   strcat(fileresf,fileres);
+           } /* k12 */
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+         } /*l1 */
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+       }/* k1 */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+       /* } */ /* loop covariates */
    }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   free_vector(xp,1,npar);
-   if (mobilav!=0) {
+   fclose(ficresprob);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprobcov);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   fclose(ficresprobcor);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   fflush(ficgp);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   fflush(fichtmcov);
-     }
+ }
-   }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /******************* Printing html file ***********/
-   if (stepm<=12) stepsize=1;
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   if(estepm < stepm){
+                   int lastpass, int stepm, int weightopt, char model[],\
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   }
+                   int popforecast, int estepm ,\
-   else  hstepm=estepm;
+                   double jprev1, double mprev1,double anprev1, \
+                   double jprev2, double mprev2,double anprev2){
-   hstepm=hstepm/stepm;
+   int jj1, k1, i1, cpt;
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-                                fractional in yp1 */
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   anprojmean=yp;
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   yp2=modf((yp1*12),&yp);
+ </ul>");
-   mprojmean=yp;
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-   yp1=modf((yp2*30.5),&yp);
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-   jprojmean=yp;
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   if(jprojmean==0) jprojmean=1;
+    fprintf(fichtm,"\
-   if(mprojmean==0) jprojmean=1;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   i1=cptcoveff;
+    fprintf(fichtm,"\
-   if (cptcovn < 1){i1=1;}
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+    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): \
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
- /*            if (h==(int)(YEARM*yearp)){ */
+    fprintf(fichtm,"\
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+  - Population projections by age and states: \
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-       k=k+1;
-       fprintf(ficresf,"\n#******");
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  m=pow(2,cptcoveff);
-       }
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-       fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+  jj1=0;
-       for(j=1; j<=nlstate+ndeath;j++){
+  for(k1=1; k1<=m;k1++){
-         for(i=1; i<=nlstate;i++)
+    for(i1=1; i1<=ncodemax[k1];i1++){
-           fprintf(ficresf," p%d%d",i,j);
+      jj1++;
-         fprintf(ficresf," p.%d",j);
+      if (cptcovn > 0) {
-       }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-         fprintf(ficresf,"\n");
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+      /* Pij */
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+      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> \
-           nhstepm = nhstepm/hstepm;
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      /* Quasi-incidences */
-           oldm=oldms;savm=savms;
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-           for (h=0; h<=nhstepm; h++){
+        /* Period (stable) prevalence in each health state */
-             if (h*hstepm/YEARM*stepm ==yearp) {
+        for(cpt=1; cpt<=nlstate;cpt++){
-               fprintf(ficresf,"\n");
+          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(j=1;j<=cptcoveff;j++)
+ <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(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+        }
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-             }
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-             for(j=1; j<=nlstate+ndeath;j++) {
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-               ppij=0.;
+      }
-               for(i=1; i<=nlstate;i++) {
+    } /* end i1 */
-                 if (mobilav==1)
+  }/* End k1 */
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+  fprintf(fichtm,"</ul>");
-                 else {
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-                 }
+  fprintf(fichtm,"\
-                 if (h*hstepm/YEARM*stepm== yearp) {
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-                 }
-               } /* end i */
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               if (h*hstepm/YEARM*stepm==yearp) {
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-                 fprintf(ficresf," %.3f", ppij);
+  fprintf(fichtm,"\
-               }
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-             }/* end j */
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-           } /* end h */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  fprintf(fichtm,"\
-         } /* end agec */
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       } /* end yearp */
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-     } /* end cptcod */
+  fprintf(fichtm,"\
-   } /* end  cptcov */
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
-   fclose(ficresf);
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
- }
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
- /************** Forecasting *****not tested NB*************/
+  fprintf(fichtm,"\
- 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){
+  - 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"));
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+  fprintf(fichtm,"\
-   int *popage;
+  - 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",
-   double calagedatem, agelim, kk1, kk2;
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   double *popeffectif,*popcount;
+  fprintf(fichtm,"\
-   double ***p3mat,***tabpop,***tabpopprev;
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-   double ***mobaverage;
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   char filerespop[FILENAMELENGTH];
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-   agelim=AGESUP;
+ /*      <br>",fileres,fileres,fileres,fileres); */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   strcpy(filerespop,"pop");
+  m=pow(2,cptcoveff);
-   strcat(filerespop,fileres);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+  jj1=0;
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+  for(k1=1; k1<=m;k1++){
-   }
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+      jj1++;
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   if (mobilav!=0) {
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+      }
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+      for(cpt=1; cpt<=nlstate;cpt++) {
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ 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);
-   }
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-   if (stepm<=12) stepsize=1;
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
-   agelim=AGESUP;
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   hstepm=1;
+    } /* end i1 */
-   hstepm=hstepm/stepm;
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
-   if (popforecast==1) {
+  fflush(fichtm);
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ }
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /******************* Gnuplot file **************/
-     }
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     popage=ivector(0,AGESUP);
-     popeffectif=vector(0,AGESUP);
+   char dirfileres[132],optfileres[132];
-     popcount=vector(0,AGESUP);
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int ng=0;
-     i=1;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*     printf("Problem with file %s",optionfilegnuplot); */
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     imx=i;
+ /*   } */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+     /*#endif */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   m=pow(2,cptcoveff);
-       k=k+1;
-       fprintf(ficrespop,"\n#******");
+   strcpy(dirfileres,optionfilefiname);
-       for(j=1;j<=cptcoveff;j++) {
+   strcpy(optfileres,"vpl");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  /* 1eme*/
-       }
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-       fprintf(ficrespop,"******\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficrespop,"# Age");
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-       for (cpt=0; cpt<=0;cpt++) {
+ set ylabel \"Probability\" \n\
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+      for (i=1; i<= nlstate ; i ++) {
-           nhstepm = nhstepm/hstepm;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      }
-           oldm=oldms;savm=savms;
+      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);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-           for (h=0; h<=nhstepm; h++){
+        else fprintf(ficgp," %%*lf (%%*lf)");
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+      }
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-             }
+      for (i=1; i<= nlstate ; i ++) {
-             for(j=1; j<=nlstate+ndeath;j++) {
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-               kk1=0.;kk2=0;
+        else fprintf(ficgp," %%*lf (%%*lf)");
-               for(i=1; i<=nlstate;i++) {
+      }
-                 if (mobilav==1)
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+    }
-                 else {
+   }
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+   /*2 eme*/
-                 }
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-               }
+   for (k1=1; k1<= m ; k1 ++) {
-               if (h==(int)(calagedatem+12*cpt)){
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-                   /*fprintf(ficrespop," %.3f", kk1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+     for (i=1; i<= nlstate+1 ; i ++) {
-               }
+       k=2*i;
-             }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-             for(i=1; i<=nlstate;i++){
+       for (j=1; j<= nlstate+1 ; j ++) {
-               kk1=0.;
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-                 for(j=1; j<=nlstate;j++){
+         else fprintf(ficgp," %%*lf (%%*lf)");
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+       }
-                 }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-             }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+         else fprintf(ficgp," %%*lf (%%*lf)");
-           }
+       }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-         }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       }
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-   /******/
+         else fprintf(ficgp," %%*lf (%%*lf)");
+       }
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   }
-           nhstepm = nhstepm/hstepm;
+   /*3eme*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+   for (k1=1; k1<= m ; k1 ++) {
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-           for (h=0; h<=nhstepm; h++){
+       /*       k=2+nlstate*(2*cpt-2); */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       k=2+(nlstate+1)*(cpt-1);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-             }
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-             for(j=1; j<=nlstate+ndeath;j++) {
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-               kk1=0.;kk2=0;
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-               for(i=1; i<=nlstate;i++) {
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-               }
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-             }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       */
-         }
+       for (i=1; i< nlstate ; i ++) {
-       }
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
-    }
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-   }
+       }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+     }
-   if (popforecast==1) {
+   }
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
+   /* CV preval stable (period) */
-     free_vector(popcount,0,AGESUP);
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-   }
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       k=3;
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
-   fclose(ficrespop);
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
- } /* End of popforecast */
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter png small size 320, 240\n\
- int fileappend(FILE *fichier, char *optionfich)
+ unset log y\n\
- {
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+       for (i=1; i<= nlstate ; i ++){
-     printf("Problem with file: %s\n", optionfich);
+         if(i==1)
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-     return (0);
+         else
-   }
+           fprintf(ficgp,", '' ");
-   fflush(fichier);
+         l=(nlstate+ndeath)*(i-1)+1;
-   return (1);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
- }
+         for (j=1; j<= (nlstate-1) ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
- /**************** function prwizard **********************/
+       } /* nlstate */
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+       fprintf(ficgp,"\n");
- {
+     } /* end cpt state*/
+   } /* end covariate */
-   /* Wizard to print covariance matrix template */
+   /* proba elementaires */
-   char ca[32], cb[32], cc[32];
+   for(i=1,jk=1; i <=nlstate; i++){
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+     for(k=1; k <=(nlstate+ndeath); k++){
-   int numlinepar;
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           jk++;
-   for(i=1; i <=nlstate; i++){
+           fprintf(ficgp,"\n");
-     jj=0;
+         }
-     for(j=1; j <=nlstate+ndeath; j++){
+       }
-       if(j==i) continue;
+     }
-       jj++;
+    }
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+   /*goto avoid;*/
-       printf("%1d%1d",i,j);
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-       fprintf(ficparo,"%1d%1d",i,j);
+      for(jk=1; jk <=m; jk++) {
-       for(k=1; k<=ncovmodel;k++){
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-         /*        printf(" %lf",param[i][j][k]); */
+        if (ng==2)
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-         printf(" 0.");
+        else
-         fprintf(ficparo," 0.");
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-       }
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-       printf("\n");
+        i=1;
-       fprintf(ficparo,"\n");
+        for(k2=1; k2<=nlstate; k2++) {
-     }
+          k3=i;
-   }
+          for(k=1; k<=(nlstate+ndeath); k++) {
-   printf("# Scales (for hessian or gradient estimation)\n");
+            if (k != k2){
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+              if(ng==2)
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-   for(i=1; i <=nlstate; i++){
+              else
-     jj=0;
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-     for(j=1; j <=nlstate+ndeath; j++){
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-       if(j==i) continue;
+              for(j=3; j <=ncovmodel; j++) {
-       jj++;
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-       fprintf(ficparo,"%1d%1d",i,j);
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-       printf("%1d%1d",i,j);
+                /*        ij++; */
-       fflush(stdout);
+                /* } */
-       for(k=1; k<=ncovmodel;k++){
+                /* else */
-         /*      printf(" %le",delti3[i][j][k]); */
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+              }
-         printf(" 0.");
+              fprintf(ficgp,")/(1");
-         fprintf(ficparo," 0.");
-       }
+              for(k1=1; k1 <=nlstate; k1++){
-       numlinepar++;
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-       printf("\n");
+                ij=1;
-       fprintf(ficparo,"\n");
+                for(j=3; j <=ncovmodel; j++){
-     }
+                  /* 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]]]); */
-   printf("# Covariance matrix\n");
+                  /*   ij++; */
- /* # 121 Var(a12)\n\ */
+                  /* } */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                  /* else */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- /* # 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\ */
+                fprintf(ficgp,")");
- /* # 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\ */
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-   fflush(stdout);
+              i=i+ncovmodel;
-   fprintf(ficparo,"# Covariance matrix\n");
+            }
-   /* # 121 Var(a12)\n\ */
+          } /* end k */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+        } /* end k2 */
-   /* #   ...\n\ */
+      } /* end jk */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+    } /* end ng */
+  /* avoid: */
-   for(itimes=1;itimes<=2;itimes++){
+    fflush(ficgp);
-     jj=0;
+ }  /* end gnuplot */
-     for(i=1; i <=nlstate; i++){
-       for(j=1; j <=nlstate+ndeath; j++){
-         if(j==i) continue;
+ /*************** Moving average **************/
-         for(k=1; k<=ncovmodel;k++){
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-           jj++;
-           ca[0]= k+'a'-1;ca[1]='\0';
+   int i, cpt, cptcod;
-           if(itimes==1){
+   int modcovmax =1;
-             printf("#%1d%1d%d",i,j,k);
+   int mobilavrange, mob;
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+   double age;
-           }else{
-             printf("%1d%1d%d",i,j,k);
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+                            a covariate has 2 modalities */
-             /*  printf(" %.5le",matcov[i][j]); */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-           }
-           ll=0;
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-           for(li=1;li <=nlstate; li++){
+     if(mobilav==1) mobilavrange=5; /* default */
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+     else mobilavrange=mobilav;
-               if(lj==li) continue;
+     for (age=bage; age<=fage; age++)
-               for(lk=1;lk<=ncovmodel;lk++){
+       for (i=1; i<=nlstate;i++)
-                 ll++;
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-                 if(ll<=jj){
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+     /* We keep the original values on the extreme ages bage, fage and for
-                   if(ll<jj){
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-                     if(itimes==1){
+        we use a 5 terms etc. until the borders are no more concerned.
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     */
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-                     }else{
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-                       printf(" 0.");
+         for (i=1; i<=nlstate;i++){
-                       fprintf(ficparo," 0.");
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-                     }
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-                   }else{
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-                     if(itimes==1){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+               }
-                     }else{
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-                       printf(" 0.");
+           }
-                       fprintf(ficparo," 0.");
+         }
-                     }
+       }/* end age */
-                   }
+     }/* end mob */
-                 }
+   }else return -1;
-               } /* end lk */
+   return 0;
-             } /* end lj */
+ }/* End movingaverage */
-           } /* end li */
-           printf("\n");
-           fprintf(ficparo,"\n");
+ /************** Forecasting ******************/
-           numlinepar++;
+ 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){
-         } /* end k*/
+   /* proj1, year, month, day of starting projection
-       } /*end j */
+      agemin, agemax range of age
-     } /* end i */
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-   } /* end itimes */
+      anproj2 year of en of projection (same day and month as proj1).
+   */
- } /* end of prwizard */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
- /******************* Gompertz Likelihood ******************************/
+   double agec; /* generic age */
- double gompertz(double x[])
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- {
+   double *popeffectif,*popcount;
-   double A,B,L=0.0,sump=0.,num=0.;
+   double ***p3mat;
-   int i,n=0; /* n is the size of the sample */
+   double ***mobaverage;
+   char fileresf[FILENAMELENGTH];
-   for (i=0;i<=imx-1 ; i++) {
-     sump=sump+weight[i];
+   agelim=AGESUP;
-     /*    sump=sump+1;*/
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     num=num+1;
-   }
+   strcpy(fileresf,"f");
+   strcat(fileresf,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   /* for (i=0; i<=imx; i++)
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-      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]);*/
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   }
-   for (i=1;i<=imx ; i++)
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-     {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-       if (cens[i] == 1 && wav[i]>1)
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-       if (cens[i] == 0 && wav[i]>1)
+   if (mobilav!=0) {
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       if (wav[i] > 1 ) { /* ??? */
+     }
-         L=L+A*weight[i];
+   }
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-       }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-     }
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   return -2*L*num/sump;
+   else  hstepm=estepm;
- }
+   hstepm=hstepm/stepm;
- /******************* Printing html file ***********/
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                                fractional in yp1 */
-                   int lastpass, int stepm, int weightopt, char model[],\
+   anprojmean=yp;
-                   int imx,  double p[],double **matcov,double agemortsup){
+   yp2=modf((yp1*12),&yp);
-   int i,k;
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   jprojmean=yp;
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   if(jprojmean==0) jprojmean=1;
-   for (i=1;i<=2;i++)
+   if(mprojmean==0) jprojmean=1;
-     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\">");
+   i1=cptcoveff;
-   fprintf(fichtm,"</ul>");
+   if (cptcovn < 1){i1=1;}
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-  for (k=agegomp;k<(agemortsup-2);k++)
+ /*            if (h==(int)(YEARM*yearp)){ */
-    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
-   fflush(fichtm);
+       fprintf(ficresf,"\n#******");
- }
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- /******************* Gnuplot file **************/
+       }
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+       fprintf(ficresf,"******\n");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   char dirfileres[132],optfileres[132];
+       for(j=1; j<=nlstate+ndeath;j++){
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+         for(i=1; i<=nlstate;i++)
-   int ng;
+           fprintf(ficresf," p%d%d",i,j);
+         fprintf(ficresf," p.%d",j);
+       }
-   /*#ifdef windows */
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+         fprintf(ficresf,"\n");
-     /*#endif */
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-   strcpy(dirfileres,optionfilefiname);
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-   strcpy(optfileres,"vpl");
+           nhstepm = nhstepm/hstepm;
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+           oldm=oldms;savm=savms;
-   fprintf(ficgp, "set ter png small\n set log y\n");
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   fprintf(ficgp, "set size 0.65,0.65\n");
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+           for (h=0; h<=nhstepm; h++){
+             if (h*hstepm/YEARM*stepm ==yearp) {
- }
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
- /***********************************************/
+               ppij=0.;
- /**************** Main Program *****************/
+               for(i=1; i<=nlstate;i++) {
- /***********************************************/
+                 if (mobilav==1)
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
- int main(int argc, char *argv[])
+                 else {
- {
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+                 }
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+                 if (h*hstepm/YEARM*stepm== yearp) {
-   int linei, month, year,iout;
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-   int jj, ll, li, lj, lk, imk;
+                 }
-   int numlinepar=0; /* Current linenumber of parameter file */
+               } /* end i */
-   int itimes;
+               if (h*hstepm/YEARM*stepm==yearp) {
-   int NDIM=2;
+                 fprintf(ficresf," %.3f", ppij);
+               }
-   char ca[32], cb[32], cc[32];
+             }/* end j */
-   char dummy[]="                         ";
+           } /* end h */
-   /*  FILE *fichtm; *//* Html File */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* FILE *ficgp;*/ /*Gnuplot File */
+         } /* end agec */
-   struct stat info;
+       } /* end yearp */
-   double agedeb, agefin,hf;
+     } /* end cptcod */
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   } /* end  cptcov */
-   double fret;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double **xi,tmp,delta;
+   fclose(ficresf);
-   double dum; /* Dummy variable */
+ }
-   double ***p3mat;
-   double ***mobaverage;
+ /************** Forecasting *****not tested NB*************/
-   int *indx;
+ 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){
-   char line[MAXLINE], linepar[MAXLINE];
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   char pathr[MAXLINE], pathimach[MAXLINE];
+   int *popage;
-   char **bp, *tok, *val; /* pathtot */
+   double calagedatem, agelim, kk1, kk2;
-   int firstobs=1, lastobs=10;
+   double *popeffectif,*popcount;
-   int sdeb, sfin; /* Status at beginning and end */
+   double ***p3mat,***tabpop,***tabpopprev;
-   int c,  h , cpt,l;
+   double ***mobaverage;
-   int ju,jl, mi;
+   char filerespop[FILENAMELENGTH];
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int mobilav=0,popforecast=0;
+   agelim=AGESUP;
-   int hstepm, nhstepm;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   int agemortsup;
-   float  sumlpop=0.;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   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;
+   strcpy(filerespop,"pop");
-   double bage, fage, age, agelim, agebase;
+   strcat(filerespop,fileres);
-   double ftolpl=FTOL;
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   double **prlim;
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   double *severity;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   double ***param; /* Matrix of parameters */
+   }
-   double  *p;
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   double **matcov; /* Matrix of covariance */
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
+   if (mobilav!=0) {
-   double *epj, vepp;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double kk1, kk2;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   double **ximort;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+     }
-   int *dcwave;
+   }
-   char z[1]="c", occ;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
+   agelim=AGESUP;
-   char *stratrunc;
-   int lstra;
+   hstepm=1;
+   hstepm=hstepm/stepm;
-   long total_usecs;
+   if (popforecast==1) {
- /*   setlocale (LC_ALL, ""); */
+     if((ficpop=fopen(popfile,"r"))==NULL) {
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       printf("Problem with population file : %s\n",popfile);exit(0);
- /*   textdomain (PACKAGE); */
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- /*   setlocale (LC_CTYPE, ""); */
+     }
- /*   setlocale (LC_MESSAGES, ""); */
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+     popcount=vector(0,AGESUP);
-   (void) gettimeofday(&start_time,&tzp);
-   curr_time=start_time;
+     i=1;
-   tm = *localtime(&start_time.tv_sec);
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
- /*  printf("Localtime (at start)=%s",strstart); */
+   }
- /*  tp.tv_sec = tp.tv_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       k=k+1;
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+       fprintf(ficrespop,"\n#******");
- /*   tp.tv_sec = mktime(&tmg); */
+       for(j=1;j<=cptcoveff;j++) {
- /*   strt=asctime(&tmg); */
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- /*   printf("Time(after) =%s",strstart);  */
+       }
- /*  (void) time (&time_value);
+       fprintf(ficrespop,"******\n");
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+       fprintf(ficrespop,"# Age");
- *  tm = *localtime(&time_value);
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- *  strstart=asctime(&tm);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
- */
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   nberr=0; /* Number of errors and warnings */
-   nbwarn=0;
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   getcwd(pathcd, size);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   printf("\n%s\n%s",version,fullversion);
-   if(argc <=1){
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("\nEnter the parameter file name: ");
+           oldm=oldms;savm=savms;
-     fgets(pathr,FILENAMELENGTH,stdin);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     i=strlen(pathr);
-     if(pathr[i-1]=='\n')
+           for (h=0; h<=nhstepm; h++){
-       pathr[i-1]='\0';
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-    for (tok = pathr; tok != NULL; ){
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       printf("Pathr |%s|\n",pathr);
+             }
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+             for(j=1; j<=nlstate+ndeath;j++) {
-       printf("val= |%s| pathr=%s\n",val,pathr);
+               kk1=0.;kk2=0;
-       strcpy (pathtot, val);
+               for(i=1; i<=nlstate;i++) {
-       if(pathr[0] == '\0') break; /* Dirty */
+                 if (mobilav==1)
-     }
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   }
+                 else {
-   else{
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-     strcpy(pathtot,argv[1]);
+                 }
-   }
+               }
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+               if (h==(int)(calagedatem+12*cpt)){
-   /*cygwin_split_path(pathtot,path,optionfile);
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+                   /*fprintf(ficrespop," %.3f", kk1);
-   /* cutv(path,optionfile,pathtot,'\\');*/
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
-   /* Split argv[0], imach program to get pathimach */
+             }
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+             for(i=1; i<=nlstate;i++){
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+               kk1=0.;
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+                 for(j=1; j<=nlstate;j++){
-  /*   strcpy(pathimach,argv[0]); */
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+                 }
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+             }
-   chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-     printf("Current directory %s!\n",pathcd);
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   strcpy(command,"mkdir ");
+           }
-   strcat(command,optionfilefiname);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   if((outcmd=system(command)) != 0){
+         }
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+       }
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     /* fclose(ficlog); */
+   /******/
- /*     exit(1); */
-   }
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- /*     perror("mkdir"); */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- /*   } */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   /*-------- arguments in the command line --------*/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* Log file */
+           oldm=oldms;savm=savms;
-   strcat(filelog, optionfilefiname);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   strcat(filelog,".log");    /* */
+           for (h=0; h<=nhstepm; h++){
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-     printf("Problem with logfile %s\n",filelog);
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     goto end;
+             }
-   }
+             for(j=1; j<=nlstate+ndeath;j++) {
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+               kk1=0.;kk2=0;
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+               for(i=1; i<=nlstate;i++) {
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+               }
-  path=%s \n\
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-  optionfile=%s\n\
+             }
-  optionfilext=%s\n\
+           }
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   printf("Local time (at start):%s",strstart);
+       }
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+    }
-   fflush(ficlog);
+   }
- /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /* */
+   if (popforecast==1) {
-   strcpy(fileres,"r");
+     free_ivector(popage,0,AGESUP);
-   strcat(fileres, optionfilefiname);
+     free_vector(popeffectif,0,AGESUP);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+     free_vector(popcount,0,AGESUP);
+   }
-   /*---------arguments file --------*/
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+   fclose(ficrespop);
-     printf("Problem with optionfile %s\n",optionfile);
+ } /* End of popforecast */
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-     fflush(ficlog);
+ int fileappend(FILE *fichier, char *optionfich)
-     goto end;
+ {
-   }
+   if((fichier=fopen(optionfich,"a"))==NULL) {
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
-   strcpy(filereso,"o");
+   }
-   strcat(filereso,fileres);
+   fflush(fichier);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+   return (1);
-     printf("Problem with Output resultfile: %s\n", filereso);
+ }
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-     fflush(ficlog);
-     goto end;
+ /**************** function prwizard **********************/
-   }
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
-   /* Reads comments: lines beginning with '#' */
-   numlinepar=0;
+   /* Wizard to print covariance matrix template */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   char ca[32], cb[32];
-     fgets(line, MAXLINE, ficpar);
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-     numlinepar++;
+   int numlinepar;
-     puts(line);
-     fputs(line,ficparo);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fputs(line,ficlog);
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   }
+   for(i=1; i <=nlstate; i++){
-   ungetc(c,ficpar);
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-   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);
+       if(j==i) continue;
-   numlinepar++;
+       jj++;
-   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);
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       printf("%1d%1d",i,j);
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       fprintf(ficparo,"%1d%1d",i,j);
-   fflush(ficlog);
+       for(k=1; k<=ncovmodel;k++){
-   while((c=getc(ficpar))=='#' && c!= EOF){
+         /*        printf(" %lf",param[i][j][k]); */
-     ungetc(c,ficpar);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-     fgets(line, MAXLINE, ficpar);
+         printf(" 0.");
-     numlinepar++;
+         fprintf(ficparo," 0.");
-     puts(line);
+       }
-     fputs(line,ficparo);
+       printf("\n");
-     fputs(line,ficlog);
+       fprintf(ficparo,"\n");
-   }
+     }
-   ungetc(c,ficpar);
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   covar=matrix(0,NCOVMAX,1,n);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+   for(i=1; i <=nlstate; i++){
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+       if(j==i) continue;
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       jj++;
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       fprintf(ficparo,"%1d%1d",i,j);
+       printf("%1d%1d",i,j);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       fflush(stdout);
-   delti=delti3[1][1];
+       for(k=1; k<=ncovmodel;k++){
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+         /*      printf(" %le",delti3[i][j][k]); */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+         printf(" 0.");
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+         fprintf(ficparo," 0.");
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       }
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       numlinepar++;
-     fclose (ficparo);
+       printf("\n");
-     fclose (ficlog);
+       fprintf(ficparo,"\n");
-     goto end;
+     }
-     exit(0);
+   }
-   }
+   printf("# Covariance matrix\n");
-   else if(mle==-3) {
+ /* # 121 Var(a12)\n\ */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ /* # 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\ */
-   }
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-   else{
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-     /* Read guess parameters */
+   fflush(stdout);
-     /* Reads comments: lines beginning with '#' */
+   fprintf(ficparo,"# Covariance matrix\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   /* # 121 Var(a12)\n\ */
-       ungetc(c,ficpar);
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-       fgets(line, MAXLINE, ficpar);
+   /* #   ...\n\ */
-       numlinepar++;
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-       puts(line);
-       fputs(line,ficparo);
+   for(itimes=1;itimes<=2;itimes++){
-       fputs(line,ficlog);
+     jj=0;
-     }
+     for(i=1; i <=nlstate; i++){
-     ungetc(c,ficpar);
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         for(k=1; k<=ncovmodel;k++){
-     for(i=1; i <=nlstate; i++){
+           jj++;
-       j=0;
+           ca[0]= k+'a'-1;ca[1]='\0';
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+           if(itimes==1){
-         if(jj==i) continue;
+             printf("#%1d%1d%d",i,j,k);
-         j++;
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+           }else{
-         if ((i1 != i) && (j1 != j)){
+             printf("%1d%1d%d",i,j,k);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
- It might be a problem of design; if ncovcol and the model are correct\n \
+             /*  printf(" %.5le",matcov[i][j]); */
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+           }
-           exit(1);
+           ll=0;
-         }
+           for(li=1;li <=nlstate; li++){
-         fprintf(ficparo,"%1d%1d",i1,j1);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-         if(mle==1)
+               if(lj==li) continue;
-           printf("%1d%1d",i,j);
+               for(lk=1;lk<=ncovmodel;lk++){
-         fprintf(ficlog,"%1d%1d",i,j);
+                 ll++;
-         for(k=1; k<=ncovmodel;k++){
+                 if(ll<=jj){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-           if(mle==1){
+                   if(ll<jj){
-             printf(" %lf",param[i][j][k]);
+                     if(itimes==1){
-             fprintf(ficlog," %lf",param[i][j][k]);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-           }
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-           else
+                     }else{
-             fprintf(ficlog," %lf",param[i][j][k]);
+                       printf(" 0.");
-           fprintf(ficparo," %lf",param[i][j][k]);
+                       fprintf(ficparo," 0.");
-         }
+                     }
-         fscanf(ficpar,"\n");
+                   }else{
-         numlinepar++;
+                     if(itimes==1){
-         if(mle==1)
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-           printf("\n");
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-         fprintf(ficlog,"\n");
+                     }else{
-         fprintf(ficparo,"\n");
+                       printf(" 0.");
-       }
+                       fprintf(ficparo," 0.");
-     }
+                     }
-     fflush(ficlog);
+                   }
+                 }
-     p=param[1][1];
+               } /* end lk */
+             } /* end lj */
-     /* Reads comments: lines beginning with '#' */
+           } /* end li */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           printf("\n");
-       ungetc(c,ficpar);
+           fprintf(ficparo,"\n");
-       fgets(line, MAXLINE, ficpar);
+           numlinepar++;
-       numlinepar++;
+         } /* end k*/
-       puts(line);
+       } /*end j */
-       fputs(line,ficparo);
+     } /* end i */
-       fputs(line,ficlog);
+   } /* end itimes */
-     }
-     ungetc(c,ficpar);
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
-     for(i=1; i <=nlstate; i++){
+ double gompertz(double x[])
-       for(j=1; j <=nlstate+ndeath-1; j++){
+ {
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   double A,B,L=0.0,sump=0.,num=0.;
-         if ((i1-i)*(j1-j)!=0){
+   int i,n=0; /* n is the size of the sample */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-           exit(1);
+   for (i=0;i<=imx-1 ; i++) {
-         }
+     sump=sump+weight[i];
-         printf("%1d%1d",i,j);
+     /*    sump=sump+1;*/
-         fprintf(ficparo,"%1d%1d",i1,j1);
+     num=num+1;
-         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]);
+   /* for (i=0; i<=imx; i++)
-           fprintf(ficparo," %le",delti3[i][j][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]);*/
-           fprintf(ficlog," %le",delti3[i][j][k]);
-         }
+   for (i=1;i<=imx ; i++)
-         fscanf(ficpar,"\n");
+     {
-         numlinepar++;
+       if (cens[i] == 1 && wav[i]>1)
-         printf("\n");
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-         fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+       if (cens[i] == 0 && wav[i]>1)
-       }
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-     }
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-     fflush(ficlog);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     delti=delti3[1][1];
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-     /* 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){
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   return -2*L*num/sump;
-       numlinepar++;
+ }
-       puts(line);
-       fputs(line,ficparo);
+ #ifdef GSL
-       fputs(line,ficlog);
+ /******************* Gompertz_f Likelihood ******************************/
-     }
+ double gompertz_f(const gsl_vector *v, void *params)
-     ungetc(c,ficpar);
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
-     matcov=matrix(1,npar,1,npar);
+   double *x= (double *) v->data;
-     for(i=1; i <=npar; i++){
+   int i,n=0; /* n is the size of the sample */
-       fscanf(ficpar,"%s",&str);
-       if(mle==1)
+   for (i=0;i<=imx-1 ; i++) {
-         printf("%s",str);
+     sump=sump+weight[i];
-       fprintf(ficlog,"%s",str);
+     /*    sump=sump+1;*/
-       fprintf(ficparo,"%s",str);
+     num=num+1;
-       for(j=1; j <=i; j++){
+   }
-         fscanf(ficpar," %le",&matcov[i][j]);
-         if(mle==1){
-           printf(" %.5le",matcov[i][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]);*/
-         fprintf(ficlog," %.5le",matcov[i][j]);
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-         fprintf(ficparo," %.5le",matcov[i][j]);
+   for (i=1;i<=imx ; i++)
-       }
+     {
-       fscanf(ficpar,"\n");
+       if (cens[i] == 1 && wav[i]>1)
-       numlinepar++;
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       if(mle==1)
-         printf("\n");
+       if (cens[i] == 0 && wav[i]>1)
-       fprintf(ficlog,"\n");
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-       fprintf(ficparo,"\n");
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-     }
-     for(i=1; i <=npar; i++)
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-       for(j=i+1;j<=npar;j++)
+       if (wav[i] > 1 ) { /* ??? */
-         matcov[i][j]=matcov[j][i];
+         LL=LL+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-     if(mle==1)
+       }
-       printf("\n");
+     }
-     fprintf(ficlog,"\n");
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     fflush(ficlog);
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-     /*-------- Rewriting parameter file ----------*/
+   return -2*LL*num/sump;
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+ }
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+ #endif
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+ /******************* Printing html file ***********/
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+                   int lastpass, int stepm, int weightopt, char model[],\
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+                   int imx,  double p[],double **matcov,double agemortsup){
-     }
+   int i,k;
-     fprintf(ficres,"#%s\n",version);
-   }    /* End of mle != -3 */
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   /*-------- data file ----------*/
+   for (i=1;i<=2;i++)
-   if((fic=fopen(datafile,"r"))==NULL)    {
+     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]));
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   fprintf(fichtm,"</ul>");
-   }
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   n= lastobs;
-   severity = vector(1,maxwav);
+  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>");
-   outcome=imatrix(1,maxwav+1,1,n);
-   num=lvector(1,n);
+  for (k=agegomp;k<(agemortsup-2);k++)
-   moisnais=vector(1,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]);
-   annais=vector(1,n);
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+   fflush(fichtm);
-   agedc=vector(1,n);
+ }
-   cod=ivector(1,n);
-   weight=vector(1,n);
+ /******************* Gnuplot file **************/
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   mint=matrix(1,maxwav,1,n);
-   anint=matrix(1,maxwav,1,n);
+   char dirfileres[132],optfileres[132];
-   s=imatrix(1,maxwav+1,1,n);
-   tab=ivector(1,NCOVMAX);
+   int ng;
-   ncodemax=ivector(1,8);
-   i=1;
+   /*#ifdef windows */
-   linei=0;
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     /*#endif */
-     linei=linei+1;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-       if(line[j] == '\t')
+   strcpy(dirfileres,optionfilefiname);
-         line[j] = ' ';
+   strcpy(optfileres,"vpl");
-     }
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-       ;
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-     };
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-     line[j+1]=0;  /* Trims blanks at end of line */
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-     if(line[0]=='#'){
-       fprintf(ficlog,"Comment line\n%s\n",line);
+ }
-       printf("Comment line\n%s\n",line);
-       continue;
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-     }
+ {
-     for (j=maxwav;j>=1;j--){
+   /*-------- data file ----------*/
-       cutv(stra, strb,line,' ');
+   FILE *fic;
-       errno=0;
+   char dummy[]="                         ";
-       lval=strtol(strb,&endptr,10);
+   int i=0, j=0, n=0;
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   int linei, month, year,iout;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   char line[MAXLINE], linetmp[MAXLINE];
-         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);
+   char stra[MAXLINE], strb[MAXLINE];
-         exit(1);
+   char *stratrunc;
-       }
+   int lstra;
-       s[j][i]=lval;
-       strcpy(line,stra);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-       cutv(stra, strb,line,' ');
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       }
+   }
-       else  if(iout=sscanf(strb,"%s.") != 0){
-         month=99;
+   i=1;
-         year=9999;
+   linei=0;
-       }else{
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-         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);
+     linei=linei+1;
-         exit(1);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-       }
+       if(line[j] == '\t')
-       anint[j][i]= (double) year;
+         line[j] = ' ';
-       mint[j][i]= (double)month;
+     }
-       strcpy(line,stra);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-     } /* ENd Waves */
+       ;
+     };
-     cutv(stra, strb,line,' ');
+     line[j+1]=0;  /* Trims blanks at end of line */
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if(line[0]=='#'){
-     }
+       fprintf(ficlog,"Comment line\n%s\n",line);
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       printf("Comment line\n%s\n",line);
-       month=99;
+       continue;
-       year=9999;
+     }
-     }else{
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       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);
+     strcpy(line, linetmp);
-       exit(1);
-     }
-     andc[i]=(double) year;
+     for (j=maxwav;j>=1;j--){
-     moisdc[i]=(double) month;
+       cutv(stra, strb, line, ' ');
-     strcpy(line,stra);
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
-     cutv(stra, strb,line,' ');
+       }else{
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         errno=0;
-     }
+         lval=strtol(strb,&endptr,10);
-     else  if(iout=sscanf(strb,"%s.") != 0){
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       month=99;
+         if( strb[0]=='\0' || (*endptr != '\0')){
-       year=9999;
+           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);
-     }else{
+           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);
-       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);
+           return 1;
-       exit(1);
+         }
-     }
+       }
-     annais[i]=(double)(year);
+       s[j][i]=lval;
-     moisnais[i]=(double)(month);
-     strcpy(line,stra);
+       strcpy(line,stra);
+       cutv(stra, strb,line,' ');
-     cutv(stra, strb,line,' ');
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-     errno=0;
+       }
-     dval=strtod(strb,&endptr);
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-     if( strb[0]=='\0' || (*endptr != '\0')){
+         month=99;
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+         year=9999;
-       exit(1);
+       }else{
-     }
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     weight[i]=dval;
+         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);
-     strcpy(line,stra);
+         return 1;
+       }
-     for (j=ncovcol;j>=1;j--){
+       anint[j][i]= (double) year;
-       cutv(stra, strb,line,' ');
+       mint[j][i]= (double)month;
-       errno=0;
+       strcpy(line,stra);
-       lval=strtol(strb,&endptr,10);
+     } /* ENd Waves */
-       if( strb[0]=='\0' || (*endptr != '\0')){
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+     cutv(stra, strb,line,' ');
-         exit(1);
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-       }
+     }
-       if(lval <-1 || lval >1){
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+       month=99;
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+       year=9999;
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+     }else{
-  For example, for multinomial values like 1, 2 and 3,\n \
+       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);
-  build V1=0 V2=0 for the reference value (1),\n \
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-         V1=1 V2=0 for (2) \n \
+         return 1;
-  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 \
+     andc[i]=(double) year;
-  Exiting.\n",lval,linei, i,line,j);
+     moisdc[i]=(double) month;
-         exit(1);
+     strcpy(line,stra);
-       }
-       covar[j][i]=(double)(lval);
+     cutv(stra, strb,line,' ');
-       strcpy(line,stra);
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     lstra=strlen(stra);
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
+       month=99;
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       year=9999;
-       stratrunc = &(stra[lstra-9]);
+     }else{
-       num[i]=atol(stratrunc);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-     }
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     else
+         return 1;
-       num[i]=atol(stra);
+     }
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+     if (year==9999) {
-       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;}*/
+       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);
-     i=i+1;
+         return 1;
-   } /* End loop reading  data */
-   fclose(fic);
+     }
-   /* printf("ii=%d", ij);
+     annais[i]=(double)(year);
-      scanf("%d",i);*/
+     moisnais[i]=(double)(month);
-   imx=i-1; /* Number of individuals */
+     strcpy(line,stra);
-   /* for (i=1; i<=imx; i++){
+     cutv(stra, strb,line,' ');
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+     errno=0;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+     dval=strtod(strb,&endptr);
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+     if( strb[0]=='\0' || (*endptr != '\0')){
-     }*/
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-    /*  for (i=1; i<=imx; 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);
-      if (s[4][i]==9)  s[4][i]=-1;
+       fflush(ficlog);
-      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]));}*/
+       return 1;
+     }
-   /* for (i=1; i<=imx; i++) */
+     weight[i]=dval;
+     strcpy(line,stra);
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
-   /* Calculation of the number of parameters from char model */
+       if(strb[0]=='.') { /* Missing status */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+         lval=-1;
-   Tprod=ivector(1,15);
+       }else{
-   Tvaraff=ivector(1,15);
+         errno=0;
-   Tvard=imatrix(1,15,1,2);
+         lval=strtol(strb,&endptr,10);
-   Tage=ivector(1,15);
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+           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);
-     j=0, j1=0, k1=1, k2=1;
+           return 1;
-     j=nbocc(model,'+'); /* j=Number of '+' */
+         }
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+       }
-     cptcovn=j+1;
+       if(lval <-1 || lval >1){
-     cptcovprod=j1; /*Number of products */
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     strcpy(modelsav,model);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+  For example, for multinomial values like 1, 2 and 3,\n \
-       printf("Error. Non available option model=%s ",model);
+  build V1=0 V2=0 for the reference value (1),\n \
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+         V1=1 V2=0 for (2) \n \
-       goto end;
+  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);
-     /* This loop fills the array Tvar from the string 'model'.*/
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     for(i=(j+1); i>=1;i--){
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+  For example, for multinomial values like 1, 2 and 3,\n \
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+  build V1=0 V2=0 for the reference value (1),\n \
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         V1=1 V2=0 for (2) \n \
-       /*scanf("%d",i);*/
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       if (strchr(strb,'*')) {  /* Model includes a product */
+  output of IMaCh is often meaningless.\n \
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+         return 1;
-           cptcovprod--;
+       }
-           cutv(strb,stre,strd,'V');
+       covar[j][i]=(double)(lval);
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+       strcpy(line,stra);
-           cptcovage++;
+     }
-             Tage[cptcovage]=i;
+     lstra=strlen(stra);
-             /*printf("stre=%s ", stre);*/
-         }
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+       stratrunc = &(stra[lstra-9]);
-           cptcovprod--;
+       num[i]=atol(stratrunc);
-           cutv(strb,stre,strc,'V');
+     }
-           Tvar[i]=atoi(stre);
+     else
-           cptcovage++;
+       num[i]=atol(stra);
-           Tage[cptcovage]=i;
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-         }
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-         else {  /* Age is not in the model */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+     i=i+1;
-           Tvar[i]=ncovcol+k1;
+   } /* End loop reading  data */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
+   *imax=i-1; /* Number of individuals */
-           Tvard[k1][1]=atoi(strc); /* m*/
+   fclose(fic);
-           Tvard[k1][2]=atoi(stre); /* n */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+   return (0);
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+   /* endread: */
-           for (k=1; k<=lastobs;k++)
+     printf("Exiting readdata: ");
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+     fclose(fic);
-           k1++;
+     return (1);
-           k2=k2+2;
-         }
-       }
-       else { /* no more sum */
+ }
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ void removespace(char *str) {
-        /*  scanf("%d",i);*/
+   char *p1 = str, *p2 = str;
-       cutv(strd,strc,strb,'V');
+   do
-       Tvar[i]=atoi(strc);
+     while (*p2 == ' ')
-       }
+       p2++;
-       strcpy(modelsav,stra);
+   while (*p1++ == *p2++);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ }
-         scanf("%d",i);*/
-     } /* end of loop + */
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-   } /* end model */
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+    * - cptcovage number of covariates with age*products =2
+    * - cptcovs number of simple covariates
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+    * - 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
-   printf("cptcovprod=%d ", cptcovprod);
+    *     which is a new column after the 9 (ncovcol) variables.
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+    * - 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
-   scanf("%d ",i);*/
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-     /*  if(mle==1){*/
+  */
-   if (weightopt != 1) { /* Maximisation without weights*/
+ {
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   int i, j, k, ks;
-   }
+   int  j1, k1, k2;
-     /*-calculation of age at interview from date of interview and age at death -*/
+   char modelsav[80];
-   agev=matrix(1,maxwav,1,imx);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-   for (i=1; i<=imx; i++) {
+   /*removespace(model);*/
-     for(m=2; (m<= maxwav); m++) {
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-         anint[m][i]=9999;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-         s[m][i]=-1;
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-       }
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-         nberr++;
+                   /* including age products which are counted in cptcovage.
-         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);
+                   * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-         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);
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-         s[m][i]=-1;
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-       }
+     strcpy(modelsav,model);
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+     if (strstr(model,"AGE") !=0){
-         nberr++;
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-         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. AGE must be in lower case model=%s ",model);fflush(ficlog);
-         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]);
+       return 1;
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+     }
-       }
+     if (strstr(model,"v") !=0){
-     }
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-   }
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
-   for (i=1; i<=imx; i++)  {
+     }
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     for(m=firstpass; (m<= lastpass); m++){
+     /*   Design
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-         if (s[m][i] >= nlstate+1) {
+      *  <          ncovcol=8                >
-           if(agedc[i]>0)
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+      *   k=  1    2      3       4     5       6      7        8
-               agev[m][i]=agedc[i];
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-             else {
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-               if ((int)andc[i]!=9999){
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-                 nbwarn++;
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+      *  Tage[++cptcovage]=k
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+      *       if products, new covar are created after ncovcol with k1
-                 agev[m][i]=-1;
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-               }
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-             }
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
-         }
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-                                  years but with the precision of a month */
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      *  <          ncovcol=8                >
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-             agev[m][i]=1;
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-           else if(agev[m][i] <agemin){
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-             agemin=agev[m][i];
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+      * p Tprod[1]@2={                         6, 5}
-           }
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-           else if(agev[m][i] >agemax){
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-             agemax=agev[m][i];
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+      *How to reorganize?
-           }
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-           /*     agev[m][i] = age[i]+2*m;*/
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-         }
+      * Struct []
-         else { /* =9 */
+      */
-           agev[m][i]=1;
-           s[m][i]=-1;
+     /* This loop fills the array Tvar from the string 'model'.*/
-         }
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-       }
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-       else /*= 0 Unknown */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-         agev[m][i]=1;
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-     }
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+     /*  k=1 Tvar[1]=2 (from V2) */
-   }
+     /*  k=5 Tvar[5] */
-   for (i=1; i<=imx; i++)  {
+     /* for (k=1; k<=cptcovn;k++) { */
-     for(m=firstpass; (m<=lastpass); m++){
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-       if (s[m][i] > (nlstate+ndeath)) {
+     /*  } */
-         nberr++;
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-         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);
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-         goto end;
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-       }
+         Tvar[k]=0;
-     }
+     cptcovage=0;
-   }
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-   /*for (i=1; i<=imx; i++){
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-   for (m=firstpass; (m<lastpass); m++){
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
- }
+       /*scanf("%d",i);*/
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
- }*/
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+           /* covar is not filled and then is empty */
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           cptcovprod--;
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           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 */
-   agegomp=(int)agemin;
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-   free_vector(severity,1,maxwav);
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-   free_imatrix(outcome,1,maxwav+1,1,n);
+           /*printf("stre=%s ", stre);*/
-   free_vector(moisnais,1,n);
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-   free_vector(annais,1,n);
+           cptcovprod--;
-   /* free_matrix(mint,1,maxwav,1,n);
+           cutl(stre,strb,strc,'V');
-      free_matrix(anint,1,maxwav,1,n);*/
+           Tvar[k]=atoi(stre);
-   free_vector(moisdc,1,n);
+           cptcovage++;
-   free_vector(andc,1,n);
+           Tage[cptcovage]=k;
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-   wav=ivector(1,imx);
+           cptcovn++;
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+           cptcovprodnoage++;k1++;
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+                                   because this model-covariate is a construction we invent a new column
-   /* Concatenates waves */
+                                   ncovcol + k1
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+                                   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 */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-   Tcode=ivector(1,100);
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-   ncodemax[1]=1;
+           k2=k2+2;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+           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) */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+           for (i=1; i<=lastobs;i++){
-                                  the estimations*/
+             /* Computes the new covariate which is a product of
-   h=0;
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-   m=pow(2,cptcoveff);
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
-   for(k=1;k<=cptcoveff; k++){
+         } /* End age is not in the model */
-     for(i=1; i <=(m/pow(2,k));i++){
+       } /* End if model includes a product */
-       for(j=1; j <= ncodemax[k]; j++){
+       else { /* no more sum */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-           h++;
+        /*  scanf("%d",i);*/
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+         cutl(strd,strc,strb,'V');
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+         ks++; /**< Number of simple covariates */
-         }
+         cptcovn++;
-       }
+         Tvar[k]=atoi(strd);
-     }
+       }
-   }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-      codtab[1][2]=1;codtab[2][2]=2; */
+         scanf("%d",i);*/
-   /* for(i=1; i <=m ;i++){
+     } /* end of loop + */
-      for(k=1; k <=cptcovn; k++){
+   } /* end model */
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-      }
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-      printf("\n");
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-      }
-      scanf("%d",i);*/
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
-   /*------------ gnuplot -------------*/
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   strcpy(optionfilegnuplot,optionfilefiname);
-   if(mle==-3)
+   scanf("%d ",i);*/
-     strcat(optionfilegnuplot,"-mort");
-   strcat(optionfilegnuplot,".gp");
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   /*endread:*/
-     printf("Problem with file %s",optionfilegnuplot);
+     printf("Exiting decodemodel: ");
-   }
+     return (1);
-   else{
+ }
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-     fprintf(ficgp,"set missing 'NaNq'\n");
+ {
-   }
+   int i, m;
-   /*  fclose(ficgp);*/
-   /*--------- index.htm --------*/
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-   if(mle==-3)
+         anint[m][i]=9999;
-     strcat(optionfilehtm,"-mort");
+         s[m][i]=-1;
-   strcat(optionfilehtm,".htm");
+       }
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+         *nberr = *nberr + 1;
-   }
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+         s[m][i]=-1;
-   strcat(optionfilehtmcov,"-cov.htm");
+       }
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+         (*nberr)++;
-   }
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-   else{
+         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]);
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
- <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);
+   }
-   }
+   for (i=1; i<=imx; i++)  {
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     for(m=firstpass; (m<= lastpass); m++){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
- \n\
+         if (s[m][i] >= nlstate+1) {
- <hr  size=\"2\" color=\"#EC5E5E\">\
+           if(agedc[i]>0){
-  <ul><li><h4>Parameter files</h4>\n\
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+               agev[m][i]=agedc[i];
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+             }else {
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+               if ((int)andc[i]!=9999){
-  - Date and time at start: %s</ul>\n",\
+                 nbwarn++;
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-           fileres,fileres,\
+                 agev[m][i]=-1;
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+               }
-   fflush(fichtm);
+             }
+           } /* agedc > 0 */
-   strcpy(pathr,path);
+         }
-   strcat(pathr,optionfilefiname);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-      and prints on file fileres'p'. */
+             agev[m][i]=1;
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+           else if(agev[m][i] < *agemin){
+             *agemin=agev[m][i];
-   fprintf(fichtm,"\n");
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+           }
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+           else if(agev[m][i] >*agemax){
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+             *agemax=agev[m][i];
-           imx,agemin,agemax,jmin,jmax,jmean);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           }
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           /*     agev[m][i] = age[i]+2*m;*/
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         }
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+         else { /* =9 */
+           agev[m][i]=1;
+           s[m][i]=-1;
-   /* 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) */
+       else /*= 0 Unknown */
+         agev[m][i]=1;
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+     }
-   if (mle==-3){
+   }
-     ximort=matrix(1,NDIM,1,NDIM);
+   for (i=1; i<=imx; i++)  {
-     cens=ivector(1,n);
+     for(m=firstpass; (m<=lastpass); m++){
-     ageexmed=vector(1,n);
+       if (s[m][i] > (nlstate+ndeath)) {
-     agecens=vector(1,n);
+         (*nberr)++;
-     dcwave=ivector(1,n);
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-     for (i=1; i<=imx; i++){
+         return 1;
-       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]);*/
+   /*for (i=1; i<=imx; i++){
-           break;
+   for (m=firstpass; (m<lastpass); m++){
-         }
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-     }
+ }
-     for (i=1; i<=imx; i++) {
+ }*/
-       if (wav[i]>0){
-         ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         agecens[i]=1.;
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         if (ageexmed[i]> 1 && wav[i] > 0){
+   return (0);
-           agecens[i]=agev[mw[j][i]][i];
+  /* endread:*/
-           cens[i]= 1;
+     printf("Exiting calandcheckages: ");
-         }else if (ageexmed[i]< 1)
+     return (1);
-           cens[i]= -1;
+ }
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           cens[i]=0 ;
+ #if defined(_MSC_VER)
-       }
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-       else cens[i]=-1;
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     }
+ //#include "stdafx.h"
+ //#include <stdio.h>
-     for (i=1;i<=NDIM;i++) {
+ //#include <tchar.h>
-       for (j=1;j<=NDIM;j++)
+ //#include <windows.h>
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+ //#include <iostream>
-     }
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
-     p[1]=0.0268; p[NDIM]=0.083;
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
-     /*printf("%lf %lf", p[1], p[2]);*/
+ BOOL IsWow64()
+ {
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         BOOL bIsWow64 = FALSE;
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         //  (HANDLE, PBOOL);
-       printf("Problem with resultfile: %s\n", filerespow);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
-     }
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+         HMODULE module = GetModuleHandle(_T("kernel32"));
-     /*  for (i=1;i<=nlstate;i++)
+         const char funcName[] = "IsWow64Process";
-         for(j=1;j<=nlstate+ndeath;j++)
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+                 GetProcAddress(module, funcName);
-     */
-     fprintf(ficrespow,"\n");
+         if (NULL != fnIsWow64Process)
+         {
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+                 if (!fnIsWow64Process(GetCurrentProcess(),
-     fclose(ficrespow);
+                         &bIsWow64))
+                         //throw std::exception("Unknown error");
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+                         printf("Unknown error\n");
+         }
-     for(i=1; i <=NDIM; i++)
+         return bIsWow64 != FALSE;
-       for(j=i+1;j<=NDIM;j++)
+ }
-         matcov[i][j]=matcov[j][i];
+ #endif
-     printf("\nCovariance matrix\n ");
+ void syscompilerinfo()
-     for(i=1; i <=NDIM; i++) {
+  {
-       for(j=1;j<=NDIM;j++){
+    /* #include "syscompilerinfo.h"*/
-         printf("%f ",matcov[i][j]);
-       }
+ #if defined __INTEL_COMPILER
-       printf("\n ");
+    struct utsname sysInfo;
-     }
+ #elif defined(__GNUC__)
+ #include <gnu/libc-version.h>  /* Only on gnu */
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+    struct utsname sysInfo;
-     for (i=1;i<=NDIM;i++)
+ #endif
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ #include <stdint.h>
-     lsurv=vector(1,AGESUP);
+    int cross = CROSS;
-     lpop=vector(1,AGESUP);
+    if (cross){
-     tpop=vector(1,AGESUP);
+      printf("Cross-");
-     lsurv[agegomp]=100000;
+      fprintf(ficlog,"Cross-");
+    }
-     for (k=agegomp;k<=AGESUP;k++) {
+    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
-       agemortsup=k;
+ #if defined(__clang__)
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
-     }
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
-     for (k=agegomp;k<agemortsup;k++)
+    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
-     for (k=agegomp;k<agemortsup;k++){
+    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+ #endif
-       sumlpop=sumlpop+lpop[k];
+ #if defined(__HP_cc) || defined(__HP_aCC)
-     }
+    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
-     tpop[agegomp]=sumlpop;
+ #if defined(__IBMC__) || defined(__IBMCPP__)
-     for (k=agegomp;k<(agemortsup-3);k++){
+    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
-       /*  tpop[k+1]=2;*/
+ #endif
-       tpop[k+1]=tpop[k]-lpop[k];
+ #if defined(_MSC_VER)
-     }
+    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
-     for (k=agegomp;k<(agemortsup-2);k++)
+ #endif
-       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+    printf(" for ");fprintf(ficlog," for ");
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
-                      stepm, weightopt,\
+     // Windows (x64 and x86)
-                      model,imx,p,matcov,agemortsup);
+    printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
+ #elif __unix__ // all unices, not all compilers
-     free_vector(lsurv,1,AGESUP);
+     // Unix
-     free_vector(lpop,1,AGESUP);
+    printf("Unix ");fprintf(ficlog,"Unix ");
-     free_vector(tpop,1,AGESUP);
+ #elif __linux__
-   } /* Endof if mle==-3 */
+     // linux
+    printf("linux ");fprintf(ficlog,"linux ");
-   else{ /* For mle >=1 */
+ #elif __APPLE__
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+    printf("Mac OS ");fprintf(ficlog,"Mac OS ");
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+ #endif
-     for (k=1; k<=npar;k++)
-       printf(" %d %8.5f",k,p[k]);
+ /*  __MINGW32__   */
-     printf("\n");
+ /*  __CYGWIN__   */
-     globpr=1; /* to print the contributions */
+ /* __MINGW64__  */
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
-     for (k=1; k<=npar;k++)
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
-       printf(" %d %8.5f",k,p[k]);
+ /* _WIN64  // Defined for applications for Win64. */
-     printf("\n");
+ /* _M_X64 // Defined for compilations that target x64 processors. */
-     if(mle>=1){ /* Could be 1 or 2 */
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
+ #if UINTPTR_MAX == 0xffffffff
+    printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
-     /*--------- results files --------------*/
+ #elif UINTPTR_MAX == 0xffffffffffffffff
-     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);
+    printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ #endif
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ #if defined(__GNUC__)
-     for(i=1,jk=1; i <=nlstate; i++){
+ # if defined(__GNUC_PATCHLEVEL__)
-       for(k=1; k <=(nlstate+ndeath); k++){
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-         if (k != i) {
+                             + __GNUC_MINOR__ * 100 \
-           printf("%d%d ",i,k);
+                             + __GNUC_PATCHLEVEL__)
-           fprintf(ficlog,"%d%d ",i,k);
+ # else
-           fprintf(ficres,"%1d%1d ",i,k);
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-           for(j=1; j <=ncovmodel; j++){
+                             + __GNUC_MINOR__ * 100)
-             printf("%lf ",p[jk]);
+ # endif
-             fprintf(ficlog,"%lf ",p[jk]);
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-             fprintf(ficres,"%lf ",p[jk]);
+    fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
-             jk++;
-           }
+    if (uname(&sysInfo) != -1) {
-           printf("\n");
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-           fprintf(ficlog,"\n");
+      fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-           fprintf(ficres,"\n");
+    }
-         }
+    else
-       }
+       perror("uname() error");
-     }
+ #ifndef __INTEL_COMPILER
-     if(mle!=0){
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
-       /* Computing hessian and covariance matrix */
+    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
-       ftolhess=ftol; /* Usually correct */
+ #endif
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+ #endif
-     }
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+    //   void main()
-     printf("# Scales (for hessian or gradient estimation)\n");
+    //   {
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ #if defined(_MSC_VER)
-     for(i=1,jk=1; i <=nlstate; i++){
+    if (IsWow64()){
-       for(j=1; j <=nlstate+ndeath; j++){
+            printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-         if (j!=i) {
+            fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-           fprintf(ficres,"%1d%1d",i,j);
+    }
-           printf("%1d%1d",i,j);
+    else{
-           fprintf(ficlog,"%1d%1d",i,j);
+            printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
-           for(k=1; k<=ncovmodel;k++){
+            frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
-             printf(" %.5e",delti[jk]);
+    }
-             fprintf(ficlog," %.5e",delti[jk]);
+    //      printf("\nPress Enter to continue...");
-             fprintf(ficres," %.5e",delti[jk]);
+    //      getchar();
-             jk++;
+    //   }
-           }
-           printf("\n");
+ #endif
-           fprintf(ficlog,"\n");
-           fprintf(ficres,"\n");
-         }
+  }
-       }
-     }
+ /***********************************************/
+ /**************** Main Program *****************/
-     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");
+ int main(int argc, char *argv[])
-     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\ */
+ #ifdef GSL
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   const gsl_multimin_fminimizer_type *T;
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   size_t iteri = 0, it;
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   int rval = GSL_CONTINUE;
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+   int status = GSL_SUCCESS;
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   double ssval;
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ #endif
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     /* Just to have a covariance matrix which will be more understandable
+   int jj, ll, li, lj, lk;
-        even is we still don't want to manage dictionary of variables
+   int numlinepar=0; /* Current linenumber of parameter file */
-     */
+   int itimes;
-     for(itimes=1;itimes<=2;itimes++){
+   int NDIM=2;
-       jj=0;
+   int vpopbased=0;
-       for(i=1; i <=nlstate; i++){
-         for(j=1; j <=nlstate+ndeath; j++){
+   char ca[32], cb[32];
-           if(j==i) continue;
+   /*  FILE *fichtm; *//* Html File */
-           for(k=1; k<=ncovmodel;k++){
+   /* FILE *ficgp;*/ /*Gnuplot File */
-             jj++;
+   struct stat info;
-             ca[0]= k+'a'-1;ca[1]='\0';
+   double agedeb;
-             if(itimes==1){
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-               if(mle>=1)
-                 printf("#%1d%1d%d",i,j,k);
+   double fret;
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+   double dum; /* Dummy variable */
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+   double ***p3mat;
-             }else{
+   double ***mobaverage;
-               if(mle>=1)
-                 printf("%1d%1d%d",i,j,k);
+   char line[MAXLINE];
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+   char pathr[MAXLINE], pathimach[MAXLINE];
-             }
+   char *tok, *val; /* pathtot */
-             ll=0;
+   int firstobs=1, lastobs=10;
-             for(li=1;li <=nlstate; li++){
+   int c,  h , cpt;
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+   int jl;
-                 if(lj==li) continue;
+   int i1, j1, jk, stepsize;
-                 for(lk=1;lk<=ncovmodel;lk++){
+   int *tab;
-                   ll++;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-                   if(ll<=jj){
+   int mobilav=0,popforecast=0;
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+   int hstepm, nhstepm;
-                     if(ll<jj){
+   int agemortsup;
-                       if(itimes==1){
+   float  sumlpop=0.;
-                         if(mle>=1)
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-                         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);
+   double bage=0, fage=110, age, agelim, agebase;
-                       }else{
+   double ftolpl=FTOL;
-                         if(mle>=1)
+   double **prlim;
-                           printf(" %.5e",matcov[jj][ll]);
+   double ***param; /* Matrix of parameters */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   double  *p;
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   double **matcov; /* Matrix of covariance */
-                       }
+   double ***delti3; /* Scale */
-                     }else{
+   double *delti; /* Scale */
-                       if(itimes==1){
+   double ***eij, ***vareij;
-                         if(mle>=1)
+   double **varpl; /* Variances of prevalence limits by age */
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+   double *epj, vepp;
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-                       }else{
+   double **ximort;
-                         if(mle>=1)
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-                           printf(" %.5e",matcov[jj][ll]);
+   int *dcwave;
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   char z[1]="c";
-                       }
-                     }
+   /*char  *strt;*/
-                   }
+   char strtend[80];
-                 } /* end lk */
-               } /* end lj */
-             } /* end li */
+ /*   setlocale (LC_ALL, ""); */
-             if(mle>=1)
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-               printf("\n");
+ /*   textdomain (PACKAGE); */
-             fprintf(ficlog,"\n");
+ /*   setlocale (LC_CTYPE, ""); */
-             fprintf(ficres,"\n");
+ /*   setlocale (LC_MESSAGES, ""); */
-             numlinepar++;
-           } /* end k*/
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-         } /*end j */
+   rstart_time = time(NULL);
-       } /* end i */
+   /*  (void) gettimeofday(&start_time,&tzp);*/
-     } /* end itimes */
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
-     fflush(ficlog);
+   /*tml = *localtime(&start_time.tm_sec);*/
-     fflush(ficres);
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+ /*  printf("Localtime (at start)=%s",strstart); */
-       fgets(line, MAXLINE, ficpar);
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-       puts(line);
+ /*  tm = *localtime(&start_time.tm_sec); */
-       fputs(line,ficparo);
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-     }
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-     ungetc(c,ficpar);
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
-     estepm=0;
+ /*   strt=asctime(&tmg); */
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ /*   printf("Time(after) =%s",strstart);  */
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+ /*  (void) time (&time_value);
-     if (fage <= 2) {
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-       bage = ageminpar;
+ *  tm = *localtime(&time_value);
-       fage = agemaxpar;
+ *  strstart=asctime(&tm);
-     }
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
-     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);
+   nberr=0; /* Number of errors and warnings */
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   nbwarn=0;
+   getcwd(pathcd, size);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   printf("\n%s\n%s",version,fullversion);
-       fgets(line, MAXLINE, ficpar);
+   if(argc <=1){
-       puts(line);
+     printf("\nEnter the parameter file name: ");
-       fputs(line,ficparo);
+     fgets(pathr,FILENAMELENGTH,stdin);
-     }
+     i=strlen(pathr);
-     ungetc(c,ficpar);
+     if(pathr[i-1]=='\n')
+       pathr[i-1]='\0';
-     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);
+     i=strlen(pathr);
-     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);
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-     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);
+       pathr[i-1]='\0';
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    for (tok = pathr; tok != NULL; ){
-     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);
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       printf("val= |%s| pathr=%s\n",val,pathr);
-       ungetc(c,ficpar);
+       strcpy (pathtot, val);
-       fgets(line, MAXLINE, ficpar);
+       if(pathr[0] == '\0') break; /* Dirty */
-       puts(line);
+     }
-       fputs(line,ficparo);
+   }
-     }
+   else{
-     ungetc(c,ficpar);
+     strcpy(pathtot,argv[1]);
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+   /*cygwin_split_path(pathtot,path,optionfile);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+   /* Split argv[0], imach program to get pathimach */
-     fprintf(ficres,"pop_based=%d\n",popbased);
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-       ungetc(c,ficpar);
+  /*   strcpy(pathimach,argv[0]); */
-       fgets(line, MAXLINE, ficpar);
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-       puts(line);
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-       fputs(line,ficparo);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-     }
+   chdir(path); /* Can be a relative path */
-     ungetc(c,ficpar);
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+     printf("Current directory %s!\n",pathcd);
-     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);
+   strcpy(command,"mkdir ");
-     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);
+   strcat(command,optionfilefiname);
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+   if((outcmd=system(command)) != 0){
-     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);
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     /* day and month of proj2 are not used but only year anproj2.*/
+     /* fclose(ficlog); */
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+ /*     perror("mkdir"); */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ /*   } */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   /*-------- arguments in the command line --------*/
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   /* Log file */
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+   strcat(filelog, optionfilefiname);
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+   strcat(filelog,".log");    /* */
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
-    /*------------ free_vector  -------------*/
+     goto end;
-    /*  chdir(path); */
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     free_ivector(wav,1,imx);
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+  path=%s \n\
-     free_lvector(num,1,n);
+  optionfile=%s\n\
-     free_vector(agedc,1,n);
+  optionfilext=%s\n\
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
+   syscompilerinfo();
-     fclose(ficres);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     strcpy(filerespl,"pl");
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     strcat(filerespl,fileres);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+   /* */
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   strcpy(fileres,"r");
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   strcat(fileres, optionfilefiname);
-     }
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   /*---------arguments file --------*/
-     pstamp(ficrespl);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     fprintf(ficrespl,"#Age ");
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     fprintf(ficrespl,"\n");
+     fflush(ficlog);
+     /* goto end; */
-     prlim=matrix(1,nlstate,1,nlstate);
+     exit(70);
+   }
-     agebase=ageminpar;
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
-     i1=cptcoveff;
+   strcpy(filereso,"o");
-     if (cptcovn < 1){i1=1;}
+   strcat(filereso,fileres);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     printf("Problem with Output resultfile: %s\n", filereso);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-         k=k+1;
+     fflush(ficlog);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     goto end;
-         fprintf(ficrespl,"\n#******");
+   }
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
+   /* Reads comments: lines beginning with '#' */
-         for(j=1;j<=cptcoveff;j++) {
+   numlinepar=0;
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     ungetc(c,ficpar);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fgets(line, MAXLINE, ficpar);
-         }
+     numlinepar++;
-         fprintf(ficrespl,"******\n");
+     fputs(line,stdout);
-         printf("******\n");
+     fputs(line,ficparo);
-         fprintf(ficlog,"******\n");
+     fputs(line,ficlog);
+   }
-         for (age=agebase; age<=agelim; age++){
+   ungetc(c,ficpar);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           fprintf(ficrespl,"%.0f ",age );
+   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);
-           for(j=1;j<=cptcoveff;j++)
+   numlinepar++;
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   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);
-           for(i=1; i<=nlstate;i++)
+   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(ficrespl," %.5f", prlim[i][i]);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-           fprintf(ficrespl,"\n");
+   fflush(ficlog);
-         }
+   while((c=getc(ficpar))=='#' && c!= EOF){
-       }
+     ungetc(c,ficpar);
-     }
+     fgets(line, MAXLINE, ficpar);
-     fclose(ficrespl);
+     numlinepar++;
+     fputs(line, stdout);
-     /*------------- h Pij x at various ages ------------*/
+     //puts(line);
+     fputs(line,ficparo);
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     fputs(line,ficlog);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+   }
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+   ungetc(c,ficpar);
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
-     printf("Computing pij: result on file '%s' \n", filerespij);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+      v1+v2*age+v2*v3 makes cptcovn = 3
-     /*if (stepm<=24) stepsize=2;*/
+   */
+   if (strlen(model)>1)
-     agelim=AGESUP;
+     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*/
-     hstepm=stepsize*YEARM; /* Every year of age */
+   else
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     ncovmodel=2;
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-     /* hstepm=1;   aff par mois*/
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-     pstamp(ficrespij);
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     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);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     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);
-         k=k+1;
+     fflush(stdout);
-         fprintf(ficrespij,"\n#****** ");
+     fclose (ficlog);
-         for(j=1;j<=cptcoveff;j++)
+     goto end;
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   }
-         fprintf(ficrespij,"******\n");
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     fclose (ficparo);
-           oldm=oldms;savm=savms;
+     fclose (ficlog);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     goto end;
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     exit(0);
-           for(i=1; i<=nlstate;i++)
+   }
-             for(j=1; j<=nlstate+ndeath;j++)
+   else if(mle==-3) {
-               fprintf(ficrespij," %1d-%1d",i,j);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-           fprintf(ficrespij,"\n");
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-           for (h=0; h<=nhstepm; h++){
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-             for(i=1; i<=nlstate;i++)
+     matcov=matrix(1,npar,1,npar);
-               for(j=1; j<=nlstate+ndeath;j++)
+   }
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+   else{
-             fprintf(ficrespij,"\n");
+     /* Read guessed parameters */
-           }
+     /* Reads comments: lines beginning with '#' */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           fprintf(ficrespij,"\n");
+       ungetc(c,ficpar);
-         }
+       fgets(line, MAXLINE, ficpar);
-       }
+       numlinepar++;
-     }
+       fputs(line,stdout);
+       fputs(line,ficparo);
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+       fputs(line,ficlog);
+     }
-     fclose(ficrespij);
+     ungetc(c,ficpar);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1;i<=AGESUP;i++)
+     for(i=1; i <=nlstate; i++){
-       for(j=1;j<=NCOVMAX;j++)
+       j=0;
-         for(k=1;k<=NCOVMAX;k++)
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-           probs[i][j][k]=0.;
+         if(jj==i) continue;
+         j++;
-     /*---------- Forecasting ------------------*/
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+         if ((i1 != i) && (j1 != j)){
-     if(prevfcast==1){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-       /*    if(stepm ==1){*/
+ It might be a problem of design; if ncovcol and the model are correct\n \
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+           exit(1);
-       /*      }  */
+         }
-       /*      else{ */
+         fprintf(ficparo,"%1d%1d",i1,j1);
-       /*        erreur=108; */
+         if(mle==1)
-       /*        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); */
+           printf("%1d%1d",i,j);
-       /*        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); */
+         fprintf(ficlog,"%1d%1d",i,j);
-       /*      } */
+         for(k=1; k<=ncovmodel;k++){
-     }
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
-     /*---------- Health expectancies and variances ------------*/
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
-     strcpy(filerest,"t");
+           else
-     strcat(filerest,fileres);
+             fprintf(ficlog," %lf",param[i][j][k]);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+           fprintf(ficparo," %lf",param[i][j][k]);
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+         }
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+         fscanf(ficpar,"\n");
-     }
+         numlinepar++;
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+         if(mle==1)
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
-     strcpy(filerese,"e");
+       }
-     strcat(filerese,fileres);
+     }
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+     fflush(ficlog);
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     /* Reads scales values */
-     }
+     p=param[1][1];
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     strcpy(fileresstde,"stde");
+       ungetc(c,ficpar);
-     strcat(fileresstde,fileres);
+       fgets(line, MAXLINE, ficpar);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       numlinepar++;
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fputs(line,stdout);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fputs(line,ficparo);
-     }
+       fputs(line,ficlog);
-     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);
+     ungetc(c,ficpar);
-     strcpy(filerescve,"cve");
+     for(i=1; i <=nlstate; i++){
-     strcat(filerescve,fileres);
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+         if ( (i1-i) * (j1-j) != 0){
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     }
+           exit(1);
-     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);
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     strcpy(fileresv,"v");
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     strcat(fileresv,fileres);
+         for(k=1; k<=ncovmodel;k++){
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+           printf(" %le",delti3[i][j][k]);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     }
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+         }
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+         fscanf(ficpar,"\n");
+         numlinepar++;
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+         printf("\n");
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         fprintf(ficparo,"\n");
-     /*  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",\
+         fprintf(ficlog,"\n");
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+       }
-     */
+     }
+     fflush(ficlog);
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* Reads covariance matrix */
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     delti=delti3[1][1];
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
+     /* 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 '#' */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       ungetc(c,ficpar);
-         k=k+1;
+       fgets(line, MAXLINE, ficpar);
-         fprintf(ficrest,"\n#****** ");
+       numlinepar++;
-         for(j=1;j<=cptcoveff;j++)
+       fputs(line,stdout);
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fputs(line,ficparo);
-         fprintf(ficrest,"******\n");
+       fputs(line,ficlog);
+     }
-         fprintf(ficreseij,"\n#****** ");
+     ungetc(c,ficpar);
-         fprintf(ficresstdeij,"\n#****** ");
-         fprintf(ficrescveij,"\n#****** ");
+     matcov=matrix(1,npar,1,npar);
-         for(j=1;j<=cptcoveff;j++) {
+     for(i=1; i <=npar; i++)
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-           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]]);
+     for(i=1; i <=npar; i++){
-         }
+       fscanf(ficpar,"%s",str);
-         fprintf(ficreseij,"******\n");
+       if(mle==1)
-         fprintf(ficresstdeij,"******\n");
+         printf("%s",str);
-         fprintf(ficrescveij,"******\n");
+       fprintf(ficlog,"%s",str);
+       fprintf(ficparo,"%s",str);
-         fprintf(ficresvij,"\n#****** ");
+       for(j=1; j <=i; j++){
-         for(j=1;j<=cptcoveff;j++)
+         fscanf(ficpar," %le",&matcov[i][j]);
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         if(mle==1){
-         fprintf(ficresvij,"******\n");
+           printf(" %.5le",matcov[i][j]);
+         }
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-         oldm=oldms;savm=savms;
+         fprintf(ficparo," %.5le",matcov[i][j]);
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       }
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       fscanf(ficpar,"\n");
+       numlinepar++;
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       if(mle==1)
-         oldm=oldms;savm=savms;
+         printf("\n");
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+       fprintf(ficlog,"\n");
-         if(popbased==1){
+       fprintf(ficparo,"\n");
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+     }
-         }
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
-         pstamp(ficrest);
+         matcov[i][j]=matcov[j][i];
-         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);
+     if(mle==1)
-         fprintf(ficrest,"\n");
+       printf("\n");
+     fprintf(ficlog,"\n");
-         epj=vector(1,nlstate+1);
-         for(age=bage; age <=fage ;age++){
+     fflush(ficlog);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           if (popbased==1) {
+     /*-------- Rewriting parameter file ----------*/
-             if(mobilav ==0){
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-               for(i=1; i<=nlstate;i++)
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-                 prlim[i][i]=probs[(int)age][i][k];
+     strcat(rfileres,".");    /* */
-             }else{ /* mobilav */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-               for(i=1; i<=nlstate;i++)
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+       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);
-           fprintf(ficrest," %4.0f",age);
+   }    /* End of mle != -3 */
-           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];
+   n= lastobs;
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+   num=lvector(1,n);
-             }
+   moisnais=vector(1,n);
-             epj[nlstate+1] +=epj[j];
+   annais=vector(1,n);
-           }
+   moisdc=vector(1,n);
+   andc=vector(1,n);
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   agedc=vector(1,n);
-             for(j=1;j <=nlstate;j++)
+   cod=ivector(1,n);
-               vepp += vareij[i][j][(int)age];
+   weight=vector(1,n);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-           for(j=1;j <=nlstate;j++){
+   mint=matrix(1,maxwav,1,n);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+   anint=matrix(1,maxwav,1,n);
-           }
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-           fprintf(ficrest,"\n");
+   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 */
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   /* Reads data from file datafile */
-         free_vector(epj,1,nlstate+1);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-       }
+     goto end;
-     }
-     free_vector(weight,1,n);
+   /* Calculation of the number of parameters from char model */
-     free_imatrix(Tvard,1,15,1,2);
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-     free_imatrix(s,1,maxwav+1,1,n);
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-     free_matrix(anint,1,maxwav,1,n);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
-     free_matrix(mint,1,maxwav,1,n);
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     free_ivector(cod,1,n);
+         k=1 Tvar[1]=2 (from V2)
-     free_ivector(tab,1,NCOVMAX);
+     */
-     fclose(ficreseij);
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-     fclose(ficresstdeij);
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-     fclose(ficrescveij);
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
-     fclose(ficresvij);
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
-     fclose(ficrest);
+   */
-     fclose(ficpar);
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
-     /*------- Variance of period (stable) prevalence------*/
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     strcpy(fileresvpl,"vpl");
+     Tvar[3=V1*V4]=4+1 etc */
-     strcat(fileresvpl,fileres);
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-       exit(0);
+   */
-     }
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+   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.
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-         k=k+1;
+covariates (3 plus signs)
-         fprintf(ficresvpl,"\n#****** ");
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-         for(j=1;j<=cptcoveff;j++)
+                       */
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     nbwarn++;
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     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){*/
-     fclose(ficresvpl);
+   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 */
-     /*---------- End : free ----------------*/
+   }
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
-   }  /* mle==-3 arrives here for freeing */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     goto end;
-     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);
+   agegomp=(int)agemin;
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_vector(moisnais,1,n);
-     free_matrix(matcov,1,npar,1,npar);
+   free_vector(annais,1,n);
-     /*free_vector(delti,1,npar);*/
+   /* free_matrix(mint,1,maxwav,1,n);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+      free_matrix(anint,1,maxwav,1,n);*/
-     free_matrix(agev,1,maxwav,1,imx);
+   free_vector(moisdc,1,n);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_vector(andc,1,n);
+   /* */
-     free_ivector(ncodemax,1,8);
-     free_ivector(Tvar,1,15);
+   wav=ivector(1,imx);
-     free_ivector(Tprod,1,15);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     free_ivector(Tvaraff,1,15);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-     free_ivector(Tage,1,15);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     free_ivector(Tcode,1,100);
+   /* Concatenates waves */
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     free_imatrix(codtab,1,100,1,10);
+   /* */
-   fflush(fichtm);
-   fflush(ficgp);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-   if((nberr >0) || (nbwarn>0)){
+   ncodemax[1]=1;
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+   Ndum =ivector(-1,NCOVMAX);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   if (ncovmodel > 2)
-   }else{
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-     printf("End of Imach\n");
-     fprintf(ficlog,"End of Imach\n");
+   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]);*/
-   printf("See log file on %s\n",filelog);
+   h=0;
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-   (void) gettimeofday(&end_time,&tzp);
-   tm = *localtime(&end_time.tv_sec);
+   /*if (cptcovn > 0) */
-   tmg = *gmtime(&end_time.tv_sec);
-   strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   m=pow(2,cptcoveff);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   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 */
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+           h++;
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+           if (h>m)
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+             h=1;
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-   fclose(fichtm);
+            *     h     1     2     3     4
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+            *______________________________
-   fclose(fichtmcov);
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-   fclose(ficgp);
+            *     2     2     1     1     1
-   fclose(ficlog);
+            *     3 i=2 1     2     1     1
-   /*------ End -----------*/
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
-    printf("Before Current directory %s!\n",pathcd);
+            *     7 i=4 1     2     2     1
-    if(chdir(pathcd) != 0)
+            *     8     2     2     2     1
-     printf("Can't move to directory %s!\n",path);
+            *     9 i=5 1 i=3 1 i=2 1     1
-   if(getcwd(pathcd,MAXLINE) > 0)
+            *    10     2     1     1     1
-     printf("Current directory %s!\n",pathcd);
+            *    11 i=6 1     2     1     1
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+            *    12     2     2     1     1
-   sprintf(plotcmd,"gnuplot");
+            *    13 i=7 1 i=4 1     2     1
- #ifndef UNIX
+            *    14     2     1     2     1
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+            *    15 i=8 1     2     2     1
- #endif
+            *    16     2     2     2     1
-   if(!stat(plotcmd,&info)){
+            */
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+           codtab[h][k]=j;
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+           /*codtab[h][Tvar[k]]=j;*/
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+           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]]);
-     }else
+         }
-       strcpy(pplotcmd,plotcmd);
+       }
- #ifdef UNIX
+     }
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+   }
-     if(!stat(plotcmd,&info)){
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+      codtab[1][2]=1;codtab[2][2]=2; */
-     }else
+   /* for(i=1; i <=m ;i++){
-       strcpy(pplotcmd,plotcmd);
+      for(k=1; k <=cptcovn; k++){
- #endif
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-   }else
+      }
-     strcpy(pplotcmd,plotcmd);
+      printf("\n");
+      }
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+      scanf("%d",i);*/
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+  free_ivector(Ndum,-1,NCOVMAX);
-   if((outcmd=system(plotcmd)) != 0){
-     printf("\n Problem with gnuplot\n");
-   }
-   printf(" Wait...");
+   /*------------ gnuplot -------------*/
-   while (z[0] != 'q') {
+   strcpy(optionfilegnuplot,optionfilefiname);
-     /* chdir(path); */
+   if(mle==-3)
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     strcat(optionfilegnuplot,"-mort");
-     scanf("%s",z);
+   strcat(optionfilegnuplot,".gp");
- /*     if (z[0] == 'c') system("./imach"); */
-     if (z[0] == 'e') {
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+     printf("Problem with file %s",optionfilegnuplot);
-       system(optionfilehtm);
+   }
-     }
+   else{
-     else if (z[0] == 'g') system(plotcmd);
+     fprintf(ficgp,"\n# %s\n", version);
-     else if (z[0] == 'q') exit(0);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-   }
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-   end:
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-   while (z[0] != 'q') {
+   }
-     printf("\nType  q for exiting: ");
+   /*  fclose(ficgp);*/
-     scanf("%s",z);
+   /*--------- 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);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+   /* 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 */
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+ #include "hpijx.h"
+     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);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     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);
+   }
+ }

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

Removed from v.1.125
changed lines
	Added in v.1.177