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Diff for /imach/src/imach.c between versions 1.125 and 1.171

-version 1.125, 2006/04/04 15:20:31
+version 1.171, 2014/12/23 13:26:59
  Line 1
  /* $Id$
    $State$
    $Log$
+   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>
+ #else
- #define MAXLINE 256
+ #include <unistd.h>
+ #endif
- #define GNUPLOTPROGRAM "gnuplot"
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <limits.h>
- #define FILENAMELENGTH 132
+ #include <sys/types.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #if defined(__GNUC__)
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #include <sys/stat.h>
+ #include <errno.h>
- #define NINTERVMAX 8
+ /* extern int errno; */
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ /* #ifdef LINUX */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ /* #include <time.h> */
- #define MAXN 20000
+ /* #include "timeval.h" */
- #define YEARM 12. /* Number of months per year */
+ /* #else */
- #define AGESUP 130
+ /* #include <sys/time.h> */
- #define AGEBASE 40
+ /* #endif */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #ifdef UNIX
+ #include <time.h>
- #define DIRSEPARATOR '/'
- #define CHARSEPARATOR "/"
+ #ifdef GSL
- #define ODIRSEPARATOR '\\'
+ #include <gsl/gsl_errno.h>
- #else
+ #include <gsl/gsl_multimin.h>
- #define DIRSEPARATOR '\\'
+ #endif
- #define CHARSEPARATOR "\\"
- #define ODIRSEPARATOR '/'
- #endif
+ #ifdef NLOPT
+ #include <nlopt.h>
- /* $Id$ */
+ typedef struct {
- /* $State$ */
+   double (* function)(double [] );
+ } myfunc_data ;
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #endif
- char fullversion[]="$Revision$ $Date$";
- char strstart[80];
+ /* #include <libintl.h> */
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ /* #define _(String) gettext (String) */
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
- int npar=NPARMAX;
+ #define GNUPLOTPROGRAM "gnuplot"
- int nlstate=2; /* Number of live states */
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int ndeath=1; /* Number of dead states */
+ #define FILENAMELENGTH 132
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- int popbased=0;
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define NINTERVMAX 8
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int mle, weightopt;
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define MAXN 20000
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define YEARM 12. /**< Number of months per year */
- double jmean; /* Mean space between 2 waves */
+ #define AGESUP 130
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define AGEBASE 40
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #ifdef _WIN32
- FILE *ficlog, *ficrespow;
+ #define DIRSEPARATOR '\\'
- int globpr; /* Global variable for printing or not */
+ #define CHARSEPARATOR "\\"
- double fretone; /* Only one call to likelihood */
+ #define ODIRSEPARATOR '/'
- long ipmx; /* Number of contributions */
+ #else
- double sw; /* Sum of weights */
+ #define DIRSEPARATOR '/'
- char filerespow[FILENAMELENGTH];
+ #define CHARSEPARATOR "/"
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #define ODIRSEPARATOR '\\'
- FILE *ficresilk;
+ #endif
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- FILE *ficresprobmorprev;
+ /* $Id$ */
- FILE *fichtm, *fichtmcov; /* Html File */
+ /* $State$ */
- FILE *ficreseij;
- char filerese[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 *ficresstdeij;
+ char fullversion[]="$Revision$ $Date$";
- char fileresstde[FILENAMELENGTH];
+ char strstart[80];
- FILE *ficrescveij;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- char filerescve[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- FILE  *ficresvij;
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char fileresv[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- FILE  *ficresvpl;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char fileresvpl[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char title[MAXLINE];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- char command[FILENAMELENGTH];
+ int cptcov=0; /* Working variable */
- int  outcmd=0;
+ int npar=NPARMAX;
+ int nlstate=2; /* Number of live states */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int popbased=0;
- char filerest[FILENAMELENGTH];
- char fileregp[FILENAMELENGTH];
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char popfile[FILENAMELENGTH];
+ int maxwav=0; /* Maxim number of waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+                    to the likelihood and the sum of weights (done by funcone)*/
- struct timezone tzp;
+ int mle=1, weightopt=0;
- extern int gettimeofday();
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- long time_value;
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- extern long time();
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- char strcurr[80], strfor[80];
+ int countcallfunc=0;  /* Count the number of calls to func */
+ double jmean=1; /* Mean space between 2 waves */
- char *endptr;
+ double **matprod2(); /* test */
- long lval;
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- double dval;
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ /*FILE *fic ; */ /* Used in readdata only */
- #define NR_END 1
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- #define FREE_ARG char*
+ FILE *ficlog, *ficrespow;
- #define FTOL 1.0e-10
+ int globpr=0; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
- #define NRANSI
+ long ipmx=0; /* Number of contributions */
- #define ITMAX 200
+ double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
- #define TOL 2.0e-4
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
- #define CGOLD 0.3819660
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define ZEPS 1.0e-10
+ FILE *ficresprobmorprev;
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ FILE *fichtm, *fichtmcov; /* Html File */
+ FILE *ficreseij;
- #define GOLD 1.618034
+ char filerese[FILENAMELENGTH];
- #define GLIMIT 100.0
+ FILE *ficresstdeij;
- #define TINY 1.0e-20
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
- static double maxarg1,maxarg2;
+ char filerescve[FILENAMELENGTH];
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ FILE  *ficresvij;
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char fileresvpl[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- static double sqrarg;
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char command[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ int  outcmd=0;
- int imx;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- int stepm=1;
- /* Stepm, step in month: minimum step interpolation*/
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
- int estepm;
+ char fileregp[FILENAMELENGTH];
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char popfile[FILENAMELENGTH];
- int m,nb;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ /* struct timezone tzp; */
- double **pmmij, ***probs;
+ /* extern int gettimeofday(); */
- double *ageexmed,*agecens;
+ struct tm tml, *gmtime(), *localtime();
- double dateintmean=0;
+ extern time_t time();
- double *weight;
- int **s; /* Status */
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- double *agedc, **covar, idx;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ struct tm tm;
- double *lsurv, *lpop, *tpop;
+ char strcurr[80], strfor[80];
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ char *endptr;
+ long lval;
- /**************** split *************************/
+ double dval;
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- {
+ #define NR_END 1
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ #define FREE_ARG char*
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ #define FTOL 1.0e-10
-   */
-   char  *ss;                            /* pointer */
+ #define NRANSI
-   int   l1, l2;                         /* length counters */
+ #define ITMAX 200
-   l1 = strlen(path );                   /* length of path */
+ #define TOL 2.0e-4
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define CGOLD 0.3819660
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ #define ZEPS 1.0e-10
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define GOLD 1.618034
-     /* get current working directory */
+ #define GLIMIT 100.0
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define TINY 1.0e-20
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-       return( GLOCK_ERROR_GETCWD );
+ static double maxarg1,maxarg2;
-     }
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     /* got dirc from getcwd*/
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     printf(" DIRC = %s \n",dirc);
-   } else {                              /* strip direcotry from path */
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     ss++;                               /* after this, the filename */
+ #define rint(a) floor(a+0.5)
-     l2 = strlen( ss );                  /* length of filename */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ /* #define mytinydouble 1.0e-16 */
-     strcpy( name, ss );         /* save file name */
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-     dirc[l1-l2] = 0;                    /* add zero */
+ /* static double dsqrarg; */
-     printf(" DIRC2 = %s \n",dirc);
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-   }
+ static double sqrarg;
-   /* We add a separator at the end of dirc if not exists */
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   l1 = strlen( dirc );                  /* length of directory */
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ int agegomp= AGEGOMP;
-     dirc[l1] =  DIRSEPARATOR;
-     dirc[l1+1] = 0;
+ int imx;
-     printf(" DIRC3 = %s \n",dirc);
+ int stepm=1;
-   }
+ /* Stepm, step in month: minimum step interpolation*/
-   ss = strrchr( name, '.' );            /* find last / */
-   if (ss >0){
+ int estepm;
-     ss++;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     strcpy(ext,ss);                     /* save extension */
-     l1= strlen( name);
+ int m,nb;
-     l2= strlen(ss)+1;
+ long *num;
-     strncpy( finame, name, l1-l2);
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-     finame[l1-l2]= 0;
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-   }
+ double **pmmij, ***probs;
+ double *ageexmed,*agecens;
-   return( 0 );                          /* we're done */
+ double dateintmean=0;
- }
+ double *weight;
+ int **s; /* Status */
- /******************************************/
+ double *agedc;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
- void replace_back_to_slash(char *s, char*t)
+                   * covar=matrix(0,NCOVMAX,1,n);
- {
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   int i;
+ double  idx;
-   int lg=0;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-   i=0;
+ int *Ndum; /** Freq of modality (tricode */
-   lg=strlen(t);
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   for(i=0; i<= lg; i++) {
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-     (s[i] = t[i]);
+ double *lsurv, *lpop, *tpop;
-     if (t[i]== '\\') s[i]='/';
-   }
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- }
+ double ftolhess; /**< Tolerance for computing hessian */
- int nbocc(char *s, char occ)
+ /**************** split *************************/
- {
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   int i,j=0;
+ {
-   int lg=20;
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   i=0;
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   lg=strlen(s);
+   */
-   for(i=0; i<= lg; i++) {
+   char  *ss;                            /* pointer */
-   if  (s[i] == occ ) j++;
+   int   l1, l2;                         /* length counters */
-   }
-   return j;
+   l1 = strlen(path );                   /* length of path */
- }
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- void cutv(char *u,char *v, char*t, char occ)
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
- {
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-      gives u="abcedf" and v="ghi2j" */
+     /* get current working directory */
-   int i,lg,j,p=0;
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   i=0;
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   for(j=0; j<=strlen(t)-1; j++) {
+       return( GLOCK_ERROR_GETCWD );
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     }
-   }
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
-   lg=strlen(t);
+   } else {                              /* strip direcotry from path */
-   for(j=0; j<p; j++) {
+     ss++;                               /* after this, the filename */
-     (u[j] = t[j]);
+     l2 = strlen( ss );                  /* length of filename */
-   }
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-      u[p]='\0';
+     strcpy( name, ss );         /* save file name */
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-    for(j=0; j<= lg; j++) {
+     dirc[l1-l2] = 0;                    /* add zero */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     printf(" DIRC2 = %s \n",dirc);
    }
- }
+   /* We add a separator at the end of dirc if not exists */
+   l1 = strlen( dirc );                  /* length of directory */
- /********************** nrerror ********************/
+   if( dirc[l1-1] != DIRSEPARATOR ){
+     dirc[l1] =  DIRSEPARATOR;
- void nrerror(char error_text[])
+     dirc[l1+1] = 0;
- {
+     printf(" DIRC3 = %s \n",dirc);
-   fprintf(stderr,"ERREUR ...\n");
+   }
-   fprintf(stderr,"%s\n",error_text);
+   ss = strrchr( name, '.' );            /* find last / */
-   exit(EXIT_FAILURE);
+   if (ss >0){
- }
+     ss++;
- /*********************** vector *******************/
+     strcpy(ext,ss);                     /* save extension */
- double *vector(int nl, int nh)
+     l1= strlen( name);
- {
+     l2= strlen(ss)+1;
-   double *v;
+     strncpy( finame, name, l1-l2);
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     finame[l1-l2]= 0;
-   if (!v) nrerror("allocation failure in vector");
+   }
-   return v-nl+NR_END;
- }
+   return( 0 );                          /* we're done */
+ }
- /************************ free vector ******************/
- void free_vector(double*v, int nl, int nh)
- {
+ /******************************************/
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ void replace_back_to_slash(char *s, char*t)
+ {
- /************************ivector *******************************/
+   int i;
- int *ivector(long nl,long nh)
+   int lg=0;
- {
+   i=0;
-   int *v;
+   lg=strlen(t);
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   for(i=0; i<= lg; i++) {
-   if (!v) nrerror("allocation failure in ivector");
+     (s[i] = t[i]);
-   return v-nl+NR_END;
+     if (t[i]== '\\') s[i]='/';
- }
+   }
+ }
- /******************free ivector **************************/
- void free_ivector(int *v, long nl, long nh)
+ char *trimbb(char *out, char *in)
- {
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   free((FREE_ARG)(v+nl-NR_END));
+   char *s;
- }
+   s=out;
+   while (*in != '\0'){
- /************************lvector *******************************/
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- long *lvector(long nl,long nh)
+       in++;
- {
+     }
-   long *v;
+     *out++ = *in++;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   }
-   if (!v) nrerror("allocation failure in ivector");
+   *out='\0';
-   return v-nl+NR_END;
+   return s;
  }
- /******************free lvector **************************/
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- void free_lvector(long *v, long nl, long nh)
+ {
- {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
-   free((FREE_ARG)(v+nl-NR_END));
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- }
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- /******************* imatrix *******************************/
+   */
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   char *s, *t;
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   t=in;s=in;
- {
+   while ((*in != occ) && (*in != '\0')){
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+     *alocc++ = *in++;
-   int **m;
+   }
+   if( *in == occ){
-   /* allocate pointers to rows */
+     *(alocc)='\0';
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+     s=++in;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   }
-   m += NR_END;
-   m -= nrl;
+   if (s == t) {/* occ not found */
+     *(alocc-(in-s))='\0';
+     in=s;
-   /* allocate rows and set pointers to them */
+   }
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   while ( *in != '\0'){
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     *blocc++ = *in++;
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   *blocc='\0';
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   return t;
+ }
-   /* return pointer to array of pointers to rows */
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   return m;
+ {
- }
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- /****************** free_imatrix *************************/
+      gives blocc="abcdef2ghi" and alocc="j".
- void free_imatrix(m,nrl,nrh,ncl,nch)
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-       int **m;
+   */
-       long nch,ncl,nrh,nrl;
+   char *s, *t;
-      /* free an int matrix allocated by imatrix() */
+   t=in;s=in;
- {
+   while (*in != '\0'){
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+     while( *in == occ){
-   free((FREE_ARG) (m+nrl-NR_END));
+       *blocc++ = *in++;
- }
+       s=in;
+     }
- /******************* matrix *******************************/
+     *blocc++ = *in++;
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   }
- {
+   if (s == t) /* occ not found */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+     *(blocc-(in-s))='\0';
-   double **m;
+   else
+     *(blocc-(in-s)-1)='\0';
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   in=s;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   while ( *in != '\0'){
-   m += NR_END;
+     *alocc++ = *in++;
-   m -= nrl;
+   }
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   *alocc='\0';
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   return s;
-   m[nrl] += NR_END;
+ }
-   m[nrl] -= ncl;
+ int nbocc(char *s, char occ)
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ {
-   return m;
+   int i,j=0;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+   int lg=20;
-    */
+   i=0;
- }
+   lg=strlen(s);
+   for(i=0; i<= lg; i++) {
- /*************************free matrix ************************/
+   if  (s[i] == occ ) j++;
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   }
- {
+   return j;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ }
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ /* void cutv(char *u,char *v, char*t, char occ) */
+ /* { */
- /******************* ma3x *******************************/
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
- {
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ /*   int i,lg,j,p=0; */
-   double ***m;
+ /*   i=0; */
+ /*   lg=strlen(t); */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*   for(j=0; j<=lg-1; j++) { */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   m += NR_END;
+ /*   } */
-   m -= nrl;
+ /*   for(j=0; j<p; j++) { */
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*     (u[j] = t[j]); */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   } */
-   m[nrl] += NR_END;
+ /*      u[p]='\0'; */
-   m[nrl] -= ncl;
+ /*    for(j=0; j<= lg; j++) { */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
+ /*   } */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ /* } */
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   m[nrl][ncl] += NR_END;
+ #ifdef _WIN32
-   m[nrl][ncl] -= nll;
+ char * strsep(char **pp, const char *delim)
-   for (j=ncl+1; j<=nch; j++)
+ {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   char *p, *q;
-   for (i=nrl+1; i<=nrh; i++) {
+   if ((p = *pp) == NULL)
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+     return 0;
-     for (j=ncl+1; j<=nch; j++)
+   if ((q = strpbrk (p, delim)) != NULL)
-       m[i][j]=m[i][j-1]+nlay;
+   {
-   }
+     *pp = q + 1;
-   return m;
+     *q = '\0';
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   }
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   else
-   */
+     *pp = 0;
- }
+   return p;
+ }
- /*************************free ma3x ************************/
+ #endif
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
- {
+ /********************** nrerror ********************/
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ void nrerror(char error_text[])
-   free((FREE_ARG)(m+nrl-NR_END));
+ {
- }
+   fprintf(stderr,"ERREUR ...\n");
+   fprintf(stderr,"%s\n",error_text);
- /*************** function subdirf ***********/
+   exit(EXIT_FAILURE);
- char *subdirf(char fileres[])
+ }
- {
+ /*********************** vector *******************/
-   /* Caution optionfilefiname is hidden */
+ double *vector(int nl, int nh)
-   strcpy(tmpout,optionfilefiname);
+ {
-   strcat(tmpout,"/"); /* Add to the right */
+   double *v;
-   strcat(tmpout,fileres);
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   return tmpout;
+   if (!v) nrerror("allocation failure in vector");
- }
+   return v-nl+NR_END;
+ }
- /*************** function subdirf2 ***********/
- char *subdirf2(char fileres[], char *preop)
+ /************************ free vector ******************/
- {
+ void free_vector(double*v, int nl, int nh)
+ {
-   /* Caution optionfilefiname is hidden */
+   free((FREE_ARG)(v+nl-NR_END));
-   strcpy(tmpout,optionfilefiname);
+ }
-   strcat(tmpout,"/");
-   strcat(tmpout,preop);
+ /************************ivector *******************************/
-   strcat(tmpout,fileres);
+ int *ivector(long nl,long nh)
-   return tmpout;
+ {
- }
+   int *v;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- /*************** function subdirf3 ***********/
+   if (!v) nrerror("allocation failure in ivector");
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   return v-nl+NR_END;
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /******************free ivector **************************/
-   strcpy(tmpout,optionfilefiname);
+ void free_ivector(int *v, long nl, long nh)
-   strcat(tmpout,"/");
+ {
-   strcat(tmpout,preop);
+   free((FREE_ARG)(v+nl-NR_END));
-   strcat(tmpout,preop2);
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /************************lvector *******************************/
- }
+ long *lvector(long nl,long nh)
+ {
- /***************** f1dim *************************/
+   long *v;
- extern int ncom;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
- extern double *pcom,*xicom;
+   if (!v) nrerror("allocation failure in ivector");
- extern double (*nrfunc)(double []);
+   return v-nl+NR_END;
+ }
- double f1dim(double x)
- {
+ /******************free lvector **************************/
-   int j;
+ void free_lvector(long *v, long nl, long nh)
-   double f;
+ {
-   double *xt;
+   free((FREE_ARG)(v+nl-NR_END));
+ }
-   xt=vector(1,ncom);
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ /******************* imatrix *******************************/
-   f=(*nrfunc)(xt);
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   free_vector(xt,1,ncom);
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   return f;
+ {
- }
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   int **m;
- /*****************brent *************************/
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   /* allocate pointers to rows */
- {
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   int iter;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   double a,b,d,etemp;
+   m += NR_END;
-   double fu,fv,fw,fx;
+   m -= nrl;
-   double ftemp;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   double e=0.0;
+   /* allocate rows and set pointers to them */
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   a=(ax < cx ? ax : cx);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   b=(ax > cx ? ax : cx);
+   m[nrl] += NR_END;
-   x=w=v=bx;
+   m[nrl] -= ncl;
-   fw=fv=fx=(*f)(x);
-   for (iter=1;iter<=ITMAX;iter++) {
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     xm=0.5*(a+b);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   /* return pointer to array of pointers to rows */
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   return m;
-     printf(".");fflush(stdout);
+ }
-     fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+ /****************** free_imatrix *************************/
-     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);
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-     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);
+       int **m;
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+       long nch,ncl,nrh,nrl;
- #endif
+      /* free an int matrix allocated by imatrix() */
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ {
-       *xmin=x;
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-       return fx;
+   free((FREE_ARG) (m+nrl-NR_END));
-     }
+ }
-     ftemp=fu;
-     if (fabs(e) > tol1) {
+ /******************* matrix *******************************/
-       r=(x-w)*(fx-fv);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       q=(x-v)*(fx-fw);
+ {
-       p=(x-v)*q-(x-w)*r;
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-       q=2.0*(q-r);
+   double **m;
-       if (q > 0.0) p = -p;
-       q=fabs(q);
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       etemp=e;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       e=d;
+   m += NR_END;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   m -= nrl;
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       else {
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-         d=p/q;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-         u=x+d;
+   m[nrl] += NR_END;
-         if (u-a < tol2 || b-u < tol2)
+   m[nrl] -= ncl;
-           d=SIGN(tol1,xm-x);
-       }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     } else {
+   return m;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-     }
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-     fu=(*f)(u);
+    */
-     if (fu <= fx) {
+ }
-       if (u >= x) a=x; else b=x;
-       SHFT(v,w,x,u)
+ /*************************free matrix ************************/
-         SHFT(fv,fw,fx,fu)
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-         } else {
+ {
-           if (u < x) a=u; else b=u;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-           if (fu <= fw || w == x) {
+   free((FREE_ARG)(m+nrl-NR_END));
-             v=w;
+ }
-             w=u;
-             fv=fw;
+ /******************* ma3x *******************************/
-             fw=fu;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-           } else if (fu <= fv || v == x || v == w) {
+ {
-             v=u;
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-             fv=fu;
+   double ***m;
-           }
-         }
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   }
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   nrerror("Too many iterations in brent");
+   m += NR_END;
-   *xmin=x;
+   m -= nrl;
-   return fx;
- }
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- /****************** mnbrak ***********************/
+   m[nrl] += NR_END;
+   m[nrl] -= ncl;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-             double (*func)(double))
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- {
-   double ulim,u,r,q, dum;
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   double fu;
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   m[nrl][ncl] += NR_END;
-   *fa=(*func)(*ax);
+   m[nrl][ncl] -= nll;
-   *fb=(*func)(*bx);
+   for (j=ncl+1; j<=nch; j++)
-   if (*fb > *fa) {
+     m[nrl][j]=m[nrl][j-1]+nlay;
-     SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+   for (i=nrl+1; i<=nrh; i++) {
-       }
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   *cx=(*bx)+GOLD*(*bx-*ax);
+     for (j=ncl+1; j<=nch; j++)
-   *fc=(*func)(*cx);
+       m[i][j]=m[i][j-1]+nlay;
-   while (*fb > *fc) {
+   }
-     r=(*bx-*ax)*(*fb-*fc);
+   return m;
-     q=(*bx-*cx)*(*fb-*fa);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   */
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+ }
-     if ((*bx-u)*(u-*cx) > 0.0) {
-       fu=(*func)(u);
+ /*************************free ma3x ************************/
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-       fu=(*func)(u);
+ {
-       if (fu < *fc) {
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-           SHFT(*fb,*fc,fu,(*func)(u))
+   free((FREE_ARG)(m+nrl-NR_END));
-           }
+ }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-       u=ulim;
+ /*************** function subdirf ***********/
-       fu=(*func)(u);
+ char *subdirf(char fileres[])
-     } else {
+ {
-       u=(*cx)+GOLD*(*cx-*bx);
+   /* Caution optionfilefiname is hidden */
-       fu=(*func)(u);
+   strcpy(tmpout,optionfilefiname);
-     }
+   strcat(tmpout,"/"); /* Add to the right */
-     SHFT(*ax,*bx,*cx,u)
+   strcat(tmpout,fileres);
-       SHFT(*fa,*fb,*fc,fu)
+   return tmpout;
-       }
+ }
- }
+ /*************** function subdirf2 ***********/
- /*************** linmin ************************/
+ char *subdirf2(char fileres[], char *preop)
+ {
- int ncom;
- double *pcom,*xicom;
+   /* Caution optionfilefiname is hidden */
- double (*nrfunc)(double []);
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   strcat(tmpout,preop);
- {
+   strcat(tmpout,fileres);
-   double brent(double ax, double bx, double cx,
+   return tmpout;
-                double (*f)(double), double tol, double *xmin);
+ }
-   double f1dim(double x);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ /*************** function subdirf3 ***********/
-               double *fc, double (*func)(double));
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   int j;
+ {
-   double xx,xmin,bx,ax;
-   double fx,fb,fa;
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
-   ncom=n;
+   strcat(tmpout,"/");
-   pcom=vector(1,n);
+   strcat(tmpout,preop);
-   xicom=vector(1,n);
+   strcat(tmpout,preop2);
-   nrfunc=func;
+   strcat(tmpout,fileres);
-   for (j=1;j<=n;j++) {
+   return tmpout;
-     pcom[j]=p[j];
+ }
-     xicom[j]=xi[j];
-   }
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   ax=0.0;
+ {
-   xx=1.0;
+   long sec_left, days, hours, minutes;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   days = (time_sec) / (60*60*24);
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   sec_left = (time_sec) % (60*60*24);
- #ifdef DEBUG
+   hours = (sec_left) / (60*60) ;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   sec_left = (sec_left) %(60*60);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   minutes = (sec_left) /60;
- #endif
+   sec_left = (sec_left) % (60);
-   for (j=1;j<=n;j++) {
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-     xi[j] *= xmin;
+   return ascdiff;
-     p[j] += xi[j];
+ }
-   }
-   free_vector(xicom,1,n);
+ /***************** f1dim *************************/
-   free_vector(pcom,1,n);
+ extern int ncom;
- }
+ extern double *pcom,*xicom;
+ extern double (*nrfunc)(double []);
- char *asc_diff_time(long time_sec, char ascdiff[])
- {
+ double f1dim(double x)
-   long sec_left, days, hours, minutes;
+ {
-   days = (time_sec) / (60*60*24);
+   int j;
-   sec_left = (time_sec) % (60*60*24);
+   double f;
-   hours = (sec_left) / (60*60) ;
+   double *xt;
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
+   xt=vector(1,ncom);
-   sec_left = (sec_left) % (60);
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   f=(*nrfunc)(xt);
-   return ascdiff;
+   free_vector(xt,1,ncom);
- }
+   return f;
+ }
- /*************** powell ************************/
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+ /*****************brent *************************/
-             double (*func)(double []))
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
  {
-   void linmin(double p[], double xi[], int n, double *fret,
+   int iter;
-               double (*func)(double []));
+   double a,b,d,etemp;
-   int i,ibig,j;
+   double fu=0,fv,fw,fx;
-   double del,t,*pt,*ptt,*xit;
+   double ftemp=0.;
-   double fp,fptt;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   double *xits;
+   double e=0.0;
-   int niterf, itmp;
+   a=(ax < cx ? ax : cx);
-   pt=vector(1,n);
+   b=(ax > cx ? ax : cx);
-   ptt=vector(1,n);
+   x=w=v=bx;
-   xit=vector(1,n);
+   fw=fv=fx=(*f)(x);
-   xits=vector(1,n);
+   for (iter=1;iter<=ITMAX;iter++) {
-   *fret=(*func)(p);
+     xm=0.5*(a+b);
-   for (j=1;j<=n;j++) pt[j]=p[j];
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   for (*iter=1;;++(*iter)) {
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     fp=(*fret);
+     printf(".");fflush(stdout);
-     ibig=0;
+     fprintf(ficlog,".");fflush(ficlog);
-     del=0.0;
+ #ifdef DEBUGBRENT
-     last_time=curr_time;
+     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);
-     (void) gettimeofday(&curr_time,&tzp);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     printf("\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);
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-     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);
+ #endif
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-    for (i=1;i<=n;i++) {
+       *xmin=x;
-       printf(" %d %.12f",i, p[i]);
+       return fx;
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+     }
-       fprintf(ficrespow," %.12lf", p[i]);
+     ftemp=fu;
-     }
+     if (fabs(e) > tol1) {
-     printf("\n");
+       r=(x-w)*(fx-fv);
-     fprintf(ficlog,"\n");
+       q=(x-v)*(fx-fw);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+       p=(x-v)*q-(x-w)*r;
-     if(*iter <=3){
+       q=2.0*(q-r);
-       tm = *localtime(&curr_time.tv_sec);
+       if (q > 0.0) p = -p;
-       strcpy(strcurr,asctime(&tm));
+       q=fabs(q);
- /*       asctime_r(&tm,strcurr); */
+       etemp=e;
-       forecast_time=curr_time;
+       e=d;
-       itmp = strlen(strcurr);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         strcurr[itmp-1]='\0';
+       else {
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+         d=p/q;
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+         u=x+d;
-       for(niterf=10;niterf<=30;niterf+=10){
+         if (u-a < tol2 || b-u < tol2)
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+           d=SIGN(tol1,xm-x);
-         tmf = *localtime(&forecast_time.tv_sec);
+       }
- /*      asctime_r(&tmf,strfor); */
+     } else {
-         strcpy(strfor,asctime(&tmf));
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         itmp = strlen(strfor);
+     }
-         if(strfor[itmp-1]=='\n')
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-         strfor[itmp-1]='\0';
+     fu=(*f)(u);
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     if (fu <= fx) {
-         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);
+       if (u >= x) a=x; else b=x;
-       }
+       SHFT(v,w,x,u)
-     }
+         SHFT(fv,fw,fx,fu)
-     for (i=1;i<=n;i++) {
+         } else {
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+           if (u < x) a=u; else b=u;
-       fptt=(*fret);
+           if (fu <= fw || w == x) {
- #ifdef DEBUG
+             v=w;
-       printf("fret=%lf \n",*fret);
+             w=u;
-       fprintf(ficlog,"fret=%lf \n",*fret);
+             fv=fw;
- #endif
+             fw=fu;
-       printf("%d",i);fflush(stdout);
+           } else if (fu <= fv || v == x || v == w) {
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+             v=u;
-       linmin(p,xit,n,fret,func);
+             fv=fu;
-       if (fabs(fptt-(*fret)) > del) {
+           }
-         del=fabs(fptt-(*fret));
+         }
-         ibig=i;
+   }
-       }
+   nrerror("Too many iterations in brent");
- #ifdef DEBUG
+   *xmin=x;
-       printf("%d %.12e",i,(*fret));
+   return fx;
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+ }
-       for (j=1;j<=n;j++) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+ /****************** mnbrak ***********************/
-         printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-       }
+             double (*func)(double))
-       for(j=1;j<=n;j++) {
+ {
-         printf(" p=%.12e",p[j]);
+   double ulim,u,r,q, dum;
-         fprintf(ficlog," p=%.12e",p[j]);
+   double fu;
-       }
-       printf("\n");
+   *fa=(*func)(*ax);
-       fprintf(ficlog,"\n");
+   *fb=(*func)(*bx);
- #endif
+   if (*fb > *fa) {
-     }
+     SHFT(dum,*ax,*bx,dum)
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+       SHFT(dum,*fb,*fa,dum)
- #ifdef DEBUG
+       }
-       int k[2],l;
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       k[0]=1;
+   *fc=(*func)(*cx);
-       k[1]=-1;
+   while (*fb > *fc) { /* Declining fa, fb, fc */
-       printf("Max: %.12e",(*func)(p));
+     r=(*bx-*ax)*(*fb-*fc);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+     q=(*bx-*cx)*(*fb-*fa);
-       for (j=1;j<=n;j++) {
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-         printf(" %.12e",p[j]);
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-         fprintf(ficlog," %.12e",p[j]);
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-       }
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
-       printf("\n");
+       fu=(*func)(u);
-       fprintf(ficlog,"\n");
+ #ifdef DEBUG
-       for(l=0;l<=1;l++) {
+       /* f(x)=A(x-u)**2+f(u) */
-         for (j=1;j<=n;j++) {
+       double A, fparabu;
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       printf("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, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ #endif
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-       }
+       fu=(*func)(u);
- #endif
+       if (fu < *fc) {
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+           SHFT(*fb,*fc,fu,(*func)(u))
-       free_vector(xit,1,n);
+           }
-       free_vector(xits,1,n);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-       free_vector(ptt,1,n);
+       u=ulim;
-       free_vector(pt,1,n);
+       fu=(*func)(u);
-       return;
+     } else {
-     }
+       u=(*cx)+GOLD*(*cx-*bx);
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+       fu=(*func)(u);
-     for (j=1;j<=n;j++) {
+     }
-       ptt[j]=2.0*p[j]-pt[j];
+     SHFT(*ax,*bx,*cx,u)
-       xit[j]=p[j]-pt[j];
+       SHFT(*fa,*fb,*fc,fu)
-       pt[j]=p[j];
+       }
-     }
+ }
-     fptt=(*func)(ptt);
-     if (fptt < fp) {
+ /*************** linmin ************************/
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-       if (t < 0.0) {
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-         linmin(p,xit,n,fret,func);
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-         for (j=1;j<=n;j++) {
+ the value of func at the returned location p . This is actually all accomplished by calling the
-           xi[j][ibig]=xi[j][n];
+ routines mnbrak and brent .*/
-           xi[j][n]=xit[j];
+ int ncom;
-         }
+ double *pcom,*xicom;
- #ifdef DEBUG
+ double (*nrfunc)(double []);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-         for(j=1;j<=n;j++){
+ {
-           printf(" %.12e",xit[j]);
+   double brent(double ax, double bx, double cx,
-           fprintf(ficlog," %.12e",xit[j]);
+                double (*f)(double), double tol, double *xmin);
-         }
+   double f1dim(double x);
-         printf("\n");
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-         fprintf(ficlog,"\n");
+               double *fc, double (*func)(double));
- #endif
+   int j;
-       }
+   double xx,xmin,bx,ax;
-     }
+   double fx,fb,fa;
-   }
- }
+   ncom=n;
+   pcom=vector(1,n);
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   xicom=vector(1,n);
+   nrfunc=func;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   for (j=1;j<=n;j++) {
- {
+     pcom[j]=p[j];
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+     xicom[j]=xi[j];
-      matrix by transitions matrix until convergence is reached */
+   }
+   ax=0.0;
-   int i, ii,j,k;
+   xx=1.0;
-   double min, max, maxmin, maxmax,sumnew=0.;
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
-   double **matprod2();
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
-   double **out, cov[NCOVMAX], **pmij();
+ #ifdef DEBUG
-   double **newm;
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ #endif
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   for (j=1;j<=n;j++) {
-     for (j=1;j<=nlstate+ndeath;j++){
+     xi[j] *= xmin;
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     p[j] += xi[j];
-     }
+   }
+   free_vector(xicom,1,n);
-    cov[1]=1.;
+   free_vector(pcom,1,n);
+ }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-     newm=savm;
+ /*************** powell ************************/
-     /* Covariates have to be included here again */
+ /*
-      cov[2]=agefin;
+ Minimization of a function func of n variables. Input consists of an initial starting point
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-       for (k=1; k<=cptcovn;k++) {
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-         /*      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]]);*/
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-       }
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+  */
-       for (k=1; k<=cptcovprod;k++)
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+             double (*func)(double []))
+ {
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   void linmin(double p[], double xi[], int n, double *fret,
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+               double (*func)(double []));
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   int i,ibig,j;
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   double del,t,*pt,*ptt,*xit;
+   double fp,fptt;
-     savm=oldm;
+   double *xits;
-     oldm=newm;
+   int niterf, itmp;
-     maxmax=0.;
-     for(j=1;j<=nlstate;j++){
+   pt=vector(1,n);
-       min=1.;
+   ptt=vector(1,n);
-       max=0.;
+   xit=vector(1,n);
-       for(i=1; i<=nlstate; i++) {
+   xits=vector(1,n);
-         sumnew=0;
+   *fret=(*func)(p);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+     rcurr_time = time(NULL);
-         max=FMAX(max,prlim[i][j]);
+   for (*iter=1;;++(*iter)) {
-         min=FMIN(min,prlim[i][j]);
+     fp=(*fret);
-       }
+     ibig=0;
-       maxmin=max-min;
+     del=0.0;
-       maxmax=FMAX(maxmax,maxmin);
+     rlast_time=rcurr_time;
-     }
+     /* (void) gettimeofday(&curr_time,&tzp); */
-     if(maxmax < ftolpl){
+     rcurr_time = time(NULL);
-       return prlim;
+     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);
- }
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+    for (i=1;i<=n;i++) {
- /*************** transition probabilities ***************/
+       printf(" %d %.12f",i, p[i]);
+       fprintf(ficlog," %d %.12lf",i, p[i]);
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       fprintf(ficrespow," %.12lf", p[i]);
- {
+     }
-   double s1, s2;
+     printf("\n");
-   /*double t34;*/
+     fprintf(ficlog,"\n");
-   int i,j,j1, nc, ii, jj;
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
-     for(i=1; i<= nlstate; i++){
+       tml = *localtime(&rcurr_time);
-       for(j=1; j<i;j++){
+       strcpy(strcurr,asctime(&tml));
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       rforecast_time=rcurr_time;
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       itmp = strlen(strcurr);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+         strcurr[itmp-1]='\0';
-         }
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-         ps[i][j]=s2;
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       for(niterf=10;niterf<=30;niterf+=10){
-       }
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-       for(j=i+1; j<=nlstate+ndeath;j++){
+         forecast_time = *localtime(&rforecast_time);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         strcpy(strfor,asctime(&forecast_time));
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+         itmp = strlen(strfor);
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         if(strfor[itmp-1]=='\n')
-         }
+         strfor[itmp-1]='\0';
-         ps[i][j]=s2;
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-       }
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-     }
+       }
-     /*ps[3][2]=1;*/
+     }
+     for (i=1;i<=n;i++) {
-     for(i=1; i<= nlstate; i++){
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       s1=0;
+       fptt=(*fret);
-       for(j=1; j<i; j++)
+ #ifdef DEBUG
-         s1+=exp(ps[i][j]);
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         s1+=exp(ps[i][j]);
+ #endif
-       ps[i][i]=1./(s1+1.);
+       printf("%d",i);fflush(stdout);
-       for(j=1; j<i; j++)
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       linmin(p,xit,n,fret,func);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       if (fabs(fptt-(*fret)) > del) {
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         del=fabs(fptt-(*fret));
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         ibig=i;
-     } /* end i */
+       }
+ #ifdef DEBUG
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       printf("%d %.12e",i,(*fret));
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-         ps[ii][jj]=0;
+       for (j=1;j<=n;j++) {
-         ps[ii][ii]=1;
+         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(j=1;j<=n;j++) {
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+         printf(" p(%d)=%.12e",j,p[j]);
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       }
- /*       } */
+       printf("\n");
- /*       printf("\n "); */
+       fprintf(ficlog,"\n");
- /*        } */
+ #endif
- /*        printf("\n ");printf("%lf ",cov[2]); */
+     } /* end i */
-        /*
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ #ifdef DEBUG
-       goto end;*/
+       int k[2],l;
-     return ps;
+       k[0]=1;
- }
+       k[1]=-1;
+       printf("Max: %.12e",(*func)(p));
- /**************** Product of 2 matrices ******************/
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+         printf(" %.12e",p[j]);
- {
+         fprintf(ficlog," %.12e",p[j]);
-   /* 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(...) */
+       printf("\n");
-   /* in, b, out are matrice of pointers which should have been initialized
+       fprintf(ficlog,"\n");
-      before: only the contents of out is modified. The function returns
+       for(l=0;l<=1;l++) {
-      a pointer to pointers identical to out */
+         for (j=1;j<=n;j++) {
-   long i, j, k;
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-   for(i=nrl; i<= nrh; i++)
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     for(k=ncolol; k<=ncoloh; 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]);
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+         }
-         out[i][k] +=in[i][j]*b[j][k];
+         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)));
-   return out;
+       }
- }
+ #endif
- /************* Higher Matrix Product ***************/
+       free_vector(xit,1,n);
+       free_vector(xits,1,n);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       free_vector(ptt,1,n);
- {
+       free_vector(pt,1,n);
-   /* Computes the transition matrix starting at age 'age' over
+       return;
-      'nhstepm*hstepm*stepm' months (i.e. until
+     }
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-      nhstepm*hstepm matrices.
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+       ptt[j]=2.0*p[j]-pt[j];
-      (typically every 2 years instead of every month which is too big
+       xit[j]=p[j]-pt[j];
-      for the memory).
+       pt[j]=p[j];
-      Model is determined by parameters x and covariates have to be
+     }
-      included manually here.
+     fptt=(*func)(ptt);
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-      */
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-   int i, j, d, h, k;
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-   double **out, cov[NCOVMAX];
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-   double **newm;
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
-   /* Hstepm could be zero and should return the unit matrix */
+       /* Thus we compare delta(2h) with observed f1-f3 */
-   for (i=1;i<=nlstate+ndeath;i++)
+       /* or best gain on one ancient line 'del' with total  */
-     for (j=1;j<=nlstate+ndeath;j++){
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
-     }
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       t= t- del*SQR(fp-fptt);
-   for(h=1; h <=nhstepm; h++){
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-     for(d=1; d <=hstepm; d++){
+       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);
-       newm=savm;
+ #ifdef DEBUG
-       /* Covariates have to be included here again */
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-       cov[1]=1.;
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       fprintf(ficlog,"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++)
+       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+Tage[k]]=cov[2+Tage[k]]*cov[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);
-       for (k=1; k<=cptcovprod;k++)
+ #endif
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       if (t < 0.0) { /* Then we use it for last direction */
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
+         for (j=1;j<=n;j++) {
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+         }
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-       savm=oldm;
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-       oldm=newm;
-     }
+ #ifdef DEBUG
-     for(i=1; i<=nlstate+ndeath; i++)
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       for(j=1;j<=nlstate+ndeath;j++) {
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         po[i][j][h]=newm[i][j];
+         for(j=1;j<=n;j++){
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+           printf(" %.12e",xit[j]);
-          */
+           fprintf(ficlog," %.12e",xit[j]);
-       }
+         }
-   } /* end h */
+         printf("\n");
-   return po;
+         fprintf(ficlog,"\n");
- }
+ #endif
+       } /* end of t negative */
+     } /* end if (fptt < fp)  */
- /*************** log-likelihood *************/
+   }
- double func( double *x)
+ }
- {
-   int i, ii, j, k, mi, d, kk;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
-   double **out;
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-   double sw; /* Sum of weights */
+ {
-   double lli; /* Individual log likelihood */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-   int s1, s2;
+      matrix by transitions matrix until convergence is reached */
-   double bbh, survp;
-   long ipmx;
+   int i, ii,j,k;
-   /*extern weight */
+   double min, max, maxmin, maxmax,sumnew=0.;
-   /* We are differentiating ll according to initial status */
+   /* double **matprod2(); */ /* test */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   double **out, cov[NCOVMAX+1], **pmij();
-   /*for(i=1;i<imx;i++)
+   double **newm;
-     printf(" %d\n",s[4][i]);
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   */
-   cov[1]=1.;
+   for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (j=1;j<=nlstate+ndeath;j++){
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
-   if(mle==1){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   cov[1]=1.;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-           for (j=1;j<=nlstate+ndeath;j++){
+     newm=savm;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* Covariates have to be included here again */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     cov[2]=agefin;
-           }
-         for(d=0; d<dh[mi][i]; d++){
+     for (k=1; k<=cptcovn;k++) {
-           newm=savm;
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+     }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           }
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-           oldm=newm;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-         } /* end mult */
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+     savm=oldm;
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+     oldm=newm;
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     maxmax=0.;
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+     for(j=1;j<=nlstate;j++){
-          * probability in order to take into account the bias as a fraction of the way
+       min=1.;
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+       max=0.;
-          * -stepm/2 to stepm/2 .
+       for(i=1; i<=nlstate; i++) {
-          * For stepm=1 the results are the same as for previous versions of Imach.
+         sumnew=0;
-          * For stepm > 1 the results are less biased than in previous versions.
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-          */
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-         s1=s[mw[mi][i]][i];
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-         s2=s[mw[mi+1][i]][i];
+         max=FMAX(max,prlim[i][j]);
-         bbh=(double)bh[mi][i]/(double)stepm;
+         min=FMIN(min,prlim[i][j]);
-         /* bias bh is positive if real duration
+       }
-          * is higher than the multiple of stepm and negative otherwise.
+       maxmin=max-min;
-          */
+       maxmax=FMAX(maxmax,maxmin);
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+     } /* j loop */
-         if( s2 > nlstate){
+     if(maxmax < ftolpl){
-           /* i.e. if s2 is a death state and if the date of death is known
+       return prlim;
-              then the contribution to the likelihood is the probability to
+     }
-              die between last step unit time and current  step unit time,
+   } /* age loop */
-              which is also equal to probability to die before dh
+   return prlim; /* should not reach here */
-              minus probability to die before dh-stepm .
+ }
-              In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
+ /*************** transition probabilities ***************/
-         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
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-         to consider that at each interview the state was recorded
+ {
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-         introduced the exact date of death then we should have modified
+      computes the probability to be observed in state j being in state i by appying the
-         the contribution of an exact death to the likelihood. This new
+      model to the ncovmodel covariates (including constant and age).
-         contribution is smaller and very dependent of the step unit
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         stepm. It is no more the probability to die between last interview
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         and month of death but the probability to survive from last
+      ncth covariate in the global vector x is given by the formula:
-         interview up to one month before death multiplied by the
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-         probability to die within a month. Thanks to Chris
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-         Jackson for correcting this bug.  Former versions increased
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         mortality artificially. The bad side is that we add another loop
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         which slows down the processing. The difference can be up to 10%
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-         lower mortality.
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-           */
+   */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
-         } else if  (s2==-2) {
-           for (j=1,survp=0. ; j<=nlstate; j++)
+     for(i=1; i<= nlstate; i++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for(j=1; j<i;j++){
-           /*survp += out[s1][j]; */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           lli= log(survp);
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         }
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         else if  (s2==-4) {
+         }
-           for (j=3,survp=0. ; j<=nlstate; j++)
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-           lli= log(survp);
+       }
-         }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         else if  (s2==-5) {
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-           for (j=1,survp=0. ; j<=2; j++)
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-           lli= log(survp);
+         }
-         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       }
-         else{
+     }
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+     for(i=1; i<= nlstate; i++){
-         }
+       s1=0;
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       for(j=1; j<i; j++){
-         /*if(lli ==000.0)*/
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         ipmx +=1;
+       }
-         sw += weight[i];
+       for(j=i+1; j<=nlstate+ndeath; j++){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-       } /* end of wave */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-     } /* end of individual */
+       }
-   }  else if(mle==2){
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       ps[i][i]=1./(s1+1.);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       /* Computing other pijs */
-       for(mi=1; mi<= wav[i]-1; mi++){
+       for(j=1; j<i; j++)
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(j=i+1; j<=nlstate+ndeath; 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);
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-           }
+     } /* end i */
-         for(d=0; d<=dh[mi][i]; d++){
-           newm=savm;
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-           for (kk=1; kk<=cptcovage;kk++) {
+         ps[ii][jj]=0;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         ps[ii][ii]=1;
-           }
+       }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
-           oldm=newm;
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         } /* end mult */
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         s1=s[mw[mi][i]][i];
+     /*   } */
-         s2=s[mw[mi+1][i]][i];
+     /*   printf("\n "); */
-         bbh=(double)bh[mi][i]/(double)stepm;
+     /* } */
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-         ipmx +=1;
+     /*
-         sw += weight[i];
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       goto end;*/
-       } /* end of wave */
+     return ps;
-     } /* end of individual */
+ }
-   }  else if(mle==3){  /* exponential inter-extrapolation */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ /**************** Product of 2 matrices ******************/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ {
-           for (j=1;j<=nlstate+ndeath;j++){
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* in, b, out are matrice of pointers which should have been initialized
-           }
+      before: only the contents of out is modified. The function returns
-         for(d=0; d<dh[mi][i]; d++){
+      a pointer to pointers identical to out */
-           newm=savm;
+   int i, j, k;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   for(i=nrl; i<= nrh; i++)
-           for (kk=1; kk<=cptcovage;kk++) {
+     for(k=ncolol; k<=ncoloh; k++){
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       out[i][k]=0.;
-           }
+       for(j=ncl; j<=nch; j++)
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         out[i][k] +=in[i][j]*b[j][k];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
+   return out;
-           oldm=newm;
+ }
-         } /* end mult */
-         s1=s[mw[mi][i]][i];
+ /************* Higher Matrix Product ***************/
-         s2=s[mw[mi+1][i]][i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-         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;
+   /* Computes the transition matrix starting at age 'age' over
-         sw += weight[i];
+      'nhstepm*hstepm*stepm' months (i.e. until
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-       } /* end of wave */
+      nhstepm*hstepm matrices.
-     } /* end of individual */
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+      (typically every 2 years instead of every month which is too big
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+      for the memory).
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      Model is determined by parameters x and covariates have to be
-       for(mi=1; mi<= wav[i]-1; mi++){
+      included manually here.
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+      */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   int i, j, d, h, k;
-           }
+   double **out, cov[NCOVMAX+1];
-         for(d=0; d<dh[mi][i]; d++){
+   double **newm;
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   /* Hstepm could be zero and should return the unit matrix */
-           for (kk=1; kk<=cptcovage;kk++) {
+   for (i=1;i<=nlstate+ndeath;i++)
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     for (j=1;j<=nlstate+ndeath;j++){
-           }
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-           savm=oldm;
+   for(h=1; h <=nhstepm; h++){
-           oldm=newm;
+     for(d=1; d <=hstepm; d++){
-         } /* end mult */
+       newm=savm;
+       /* Covariates have to be included here again */
-         s1=s[mw[mi][i]][i];
+       cov[1]=1.;
-         s2=s[mw[mi+1][i]][i];
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-         if( s2 > nlstate){
+       for (k=1; k<=cptcovn;k++)
-           lli=log(out[s1][s2] - savm[s1][s2]);
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         }else{
+       for (k=1; k<=cptcovage;k++)
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         }
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-         ipmx +=1;
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         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("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-       } /* end of wave */
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-     } /* end of individual */
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       savm=oldm;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       oldm=newm;
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     for(i=1; i<=nlstate+ndeath; i++)
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(j=1;j<=nlstate+ndeath;j++) {
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         po[i][j][h]=newm[i][j];
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-           }
+       }
-         for(d=0; d<dh[mi][i]; d++){
+     /*printf("h=%d ",h);*/
-           newm=savm;
+   } /* end h */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ /*     printf("\n H=%d \n",h); */
-           for (kk=1; kk<=cptcovage;kk++) {
+   return po;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
-           }
+ #ifdef NLOPT
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   double fret;
-           savm=oldm;
+   double *xt;
-           oldm=newm;
+   int j;
-         } /* end mult */
+   myfunc_data *d2 = (myfunc_data *) pd;
+ /* xt = (p1-1); */
-         s1=s[mw[mi][i]][i];
+   xt=vector(1,n);
-         s2=s[mw[mi+1][i]][i];
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         ipmx +=1;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-         sw += weight[i];
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   printf("Function = %.12lf ",fret);
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-       } /* end of wave */
+   printf("\n");
-     } /* end of individual */
+  free_vector(xt,1,n);
-   } /* End of if */
+   return fret;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ }
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ #endif
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   return -l;
+ /*************** log-likelihood *************/
- }
+ double func( double *x)
+ {
- /*************** log-likelihood *************/
+   int i, ii, j, k, mi, d, kk;
- double funcone( double *x)
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
- {
+   double **out;
-   /* Same as likeli but slower because of a lot of printf and if */
+   double sw; /* Sum of weights */
-   int i, ii, j, k, mi, d, kk;
+   double lli; /* Individual log likelihood */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   int s1, s2;
-   double **out;
+   double bbh, survp;
-   double lli; /* Individual log likelihood */
+   long ipmx;
-   double llt;
+   /*extern weight */
-   int s1, s2;
+   /* We are differentiating ll according to initial status */
-   double bbh, survp;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*extern weight */
+   /*for(i=1;i<imx;i++)
-   /* We are differentiating ll according to initial status */
+     printf(" %d\n",s[4][i]);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   */
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
+   ++countcallfunc;
-   */
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   if(mle==1){
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for(mi=1; mi<= wav[i]-1; mi++){
+       /* Computes the values of the ncovmodel covariates of the model
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-         for (j=1;j<=nlstate+ndeath;j++){
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+          to be observed in j being in i according to the model.
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+        */
-         }
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-       for(d=0; d<dh[mi][i]; d++){
+         cov[2+k]=covar[Tvar[k]][i];
-         newm=savm;
+       }
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-         for (kk=1; kk<=cptcovage;kk++) {
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+          has been calculated etc */
-         }
+       for(mi=1; mi<= wav[i]-1; mi++){
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           for (j=1;j<=nlstate+ndeath;j++){
-         savm=oldm;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         oldm=newm;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } /* end mult */
+           }
+         for(d=0; d<dh[mi][i]; d++){
-       s1=s[mw[mi][i]][i];
+           newm=savm;
-       s2=s[mw[mi+1][i]][i];
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       bbh=(double)bh[mi][i]/(double)stepm;
+           for (kk=1; kk<=cptcovage;kk++) {
-       /* bias is positive if real duration
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-        * is higher than the multiple of stepm and negative otherwise.
+           }
-        */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         lli=log(out[s1][s2] - savm[s1][s2]);
+           savm=oldm;
-       } else if  (s2==-2) {
+           oldm=newm;
-         for (j=1,survp=0. ; j<=nlstate; j++)
+         } /* end mult */
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         lli= log(survp);
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-       }else if (mle==1){
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-       } else if(mle==2){
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         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 */
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-       } else if(mle==3){  /* exponential inter-extrapolation */
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         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 */
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+          * 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
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+          * -stepm/2 to stepm/2 .
-         lli=log(out[s1][s2]); /* Original formula */
+          * For stepm=1 the results are the same as for previous versions of Imach.
-       } /* End of if */
+          * For stepm > 1 the results are less biased than in previous versions.
-       ipmx +=1;
+          */
-       sw += weight[i];
+         s1=s[mw[mi][i]][i];
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         s2=s[mw[mi+1][i]][i];
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+         bbh=(double)bh[mi][i]/(double)stepm;
-       if(globpr){
+         /* bias bh is positive if real duration
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+          * is higher than the multiple of stepm and negative otherwise.
-  %11.6f %11.6f %11.6f ", \
+          */
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[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]));*/
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         if( s2 > nlstate){
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           /* i.e. if s2 is a death state and if the date of death is known
-           llt +=ll[k]*gipmx/gsw;
+              then the contribution to the likelihood is the probability to
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+              die between last step unit time and current  step unit time,
-         }
+              which is also equal to probability to die before dh
-         fprintf(ficresilk," %10.6f\n", -llt);
+              minus probability to die before dh-stepm .
-       }
+              In version up to 0.92 likelihood was computed
-     } /* end of wave */
+         as if date of death was unknown. Death was treated as any other
-   } /* end of individual */
+         health state: the date of the interview describes the actual state
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         and not the date of a change in health state. The former idea was
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         to consider that at each interview the state was recorded
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         (healthy, disable or death) and IMaCh was corrected; but when we
-   if(globpr==0){ /* First time we count the contributions and weights */
+         introduced the exact date of death then we should have modified
-     gipmx=ipmx;
+         the contribution of an exact death to the likelihood. This new
-     gsw=sw;
+         contribution is smaller and very dependent of the step unit
-   }
+         stepm. It is no more the probability to die between last interview
-   return -l;
+         and month of death but the probability to survive from last
- }
+         interview up to one month before death multiplied by the
+         probability to die within a month. Thanks to Chris
+         Jackson for correcting this bug.  Former versions increased
- /*************** function likelione ***********/
+         mortality artificially. The bad side is that we add another loop
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+         which slows down the processing. The difference can be up to 10%
- {
+         lower mortality.
-   /* This routine should help understanding what is done with
+           */
-      the selection of individuals/waves and
+           lli=log(out[s1][s2] - savm[s1][s2]);
-      to check the exact contribution to the likelihood.
-      Plotting could be done.
-    */
+         } else if  (s2==-2) {
-   int k;
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+           /*survp += out[s1][j]; */
-     strcpy(fileresilk,"ilk");
+           lli= log(survp);
-     strcat(fileresilk,fileres);
+         }
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-       printf("Problem with resultfile: %s\n", fileresilk);
+         else if  (s2==-4) {
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+           for (j=3,survp=0. ; j<=nlstate; j++)
-     }
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     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");
+           lli= log(survp);
-     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++)
+         else if  (s2==-5) {
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+           for (j=1,survp=0. ; j<=2; j++)
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   }
+           lli= log(survp);
+         }
-   *fretone=(*funcone)(p);
-   if(*globpri !=0){
+         else{
-     fclose(ficresilk);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+           /*  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 */
-     fflush(fichtm);
+         }
-   }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   return;
+         /*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); */
+         ipmx +=1;
+         sw += weight[i];
- /*********** Maximum Likelihood Estimation ***************/
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+     } /* end of individual */
- {
+   }  else if(mle==2){
-   int i,j, iter;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double **xi;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   double fret;
+       for(mi=1; mi<= wav[i]-1; mi++){
-   double fretone; /* Only one call to likelihood */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   /*  char filerespow[FILENAMELENGTH];*/
+           for (j=1;j<=nlstate+ndeath;j++){
-   xi=matrix(1,npar,1,npar);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   for (i=1;i<=npar;i++)
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for (j=1;j<=npar;j++)
+           }
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         for(d=0; d<=dh[mi][i]; d++){
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+           newm=savm;
-   strcpy(filerespow,"pow");
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   strcat(filerespow,fileres);
+           for (kk=1; kk<=cptcovage;kk++) {
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     printf("Problem with resultfile: %s\n", filerespow);
+           }
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+           savm=oldm;
-   for (i=1;i<=nlstate;i++)
+           oldm=newm;
-     for(j=1;j<=nlstate+ndeath;j++)
+         } /* end mult */
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   fprintf(ficrespow,"\n");
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+         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 */
-   free_matrix(xi,1,npar,1,npar);
+         ipmx +=1;
-   fclose(ficrespow);
+         sw += weight[i];
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       } /* end of wave */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
- }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- /**** Computes Hessian and covariance matrix ***/
+       for(mi=1; mi<= wav[i]-1; mi++){
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- {
+           for (j=1;j<=nlstate+ndeath;j++){
-   double  **a,**y,*x,pd;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double **hess;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int i, j,jk;
+           }
-   int *indx;
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+           for (kk=1; kk<=cptcovage;kk++) {
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+           }
-   double gompertz(double p[]);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   hess=matrix(1,npar,1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+           oldm=newm;
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+         } /* end mult */
-   for (i=1;i<=npar;i++){
-     printf("%d",i);fflush(stdout);
+         s1=s[mw[mi][i]][i];
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+         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;
-     /*  printf(" %f ",p[i]);
+         sw += weight[i];
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   }
+       } /* end of wave */
+     } /* end of individual */
-   for (i=1;i<=npar;i++) {
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-     for (j=1;j<=npar;j++)  {
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       if (j>i) {
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         printf(".%d%d",i,j);fflush(stdout);
+       for(mi=1; mi<= wav[i]-1; mi++){
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         hess[j][i]=hess[i][j];
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         /*printf(" %lf ",hess[i][j]);*/
+           }
-       }
+         for(d=0; d<dh[mi][i]; d++){
-     }
+           newm=savm;
-   }
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   printf("\n");
+           for (kk=1; kk<=cptcovage;kk++) {
-   fprintf(ficlog,"\n");
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   a=matrix(1,npar,1,npar);
+           savm=oldm;
-   y=matrix(1,npar,1,npar);
+           oldm=newm;
-   x=vector(1,npar);
+         } /* end mult */
-   indx=ivector(1,npar);
-   for (i=1;i<=npar;i++)
+         s1=s[mw[mi][i]][i];
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+         s2=s[mw[mi+1][i]][i];
-   ludcmp(a,npar,indx,&pd);
+         if( s2 > nlstate){
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   for (j=1;j<=npar;j++) {
+         }else{
-     for (i=1;i<=npar;i++) x[i]=0;
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-     x[j]=1;
+         }
-     lubksb(a,npar,indx,x);
+         ipmx +=1;
-     for (i=1;i<=npar;i++){
+         sw += weight[i];
-       matcov[i][j]=x[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 */
+     } /* end of individual */
-   printf("\n#Hessian matrix#\n");
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   for (i=1;i<=npar;i++) {
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     for (j=1;j<=npar;j++) {
+       for(mi=1; mi<= wav[i]-1; mi++){
-       printf("%.3e ",hess[i][j]);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+           for (j=1;j<=nlstate+ndeath;j++){
-     }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     printf("\n");
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficlog,"\n");
+           }
-   }
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   /* Recompute Inverse */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   for (i=1;i<=npar;i++)
+           for (kk=1; kk<=cptcovage;kk++) {
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   ludcmp(a,npar,indx,&pd);
+           }
-   /*  printf("\n#Hessian matrix recomputed#\n");
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   for (j=1;j<=npar;j++) {
+           savm=oldm;
-     for (i=1;i<=npar;i++) x[i]=0;
+           oldm=newm;
-     x[j]=1;
+         } /* end mult */
-     lubksb(a,npar,indx,x);
-     for (i=1;i<=npar;i++){
+         s1=s[mw[mi][i]][i];
-       y[i][j]=x[i];
+         s2=s[mw[mi+1][i]][i];
-       printf("%.3e ",y[i][j]);
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       fprintf(ficlog,"%.3e ",y[i][j]);
+         ipmx +=1;
-     }
+         sw += weight[i];
-     printf("\n");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fprintf(ficlog,"\n");
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-   }
+       } /* end of wave */
-   */
+     } /* end of individual */
+   } /* End of if */
-   free_matrix(a,1,npar,1,npar);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   free_matrix(y,1,npar,1,npar);
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   free_vector(x,1,npar);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   free_ivector(indx,1,npar);
+   return -l;
-   free_matrix(hess,1,npar,1,npar);
+ }
+ /*************** log-likelihood *************/
- }
+ double funcone( double *x)
+ {
- /*************** hessian matrix ****************/
+   /* Same as likeli but slower because of a lot of printf and if */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   int i, ii, j, k, mi, d, kk;
- {
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   int i;
+   double **out;
-   int l=1, lmax=20;
+   double lli; /* Individual log likelihood */
-   double k1,k2;
+   double llt;
-   double p2[NPARMAX+1];
+   int s1, s2;
-   double res;
+   double bbh, survp;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   /*extern weight */
-   double fx;
+   /* We are differentiating ll according to initial status */
-   int k=0,kmax=10;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   double l1;
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
-   fx=func(x);
+   */
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+   cov[1]=1.;
-   for(l=0 ; l <=lmax; l++){
-     l1=pow(10,l);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     delts=delt;
-     for(k=1 ; k <kmax; k=k+1){
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       delt = delta*(l1*k);
+     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++){
-       k1=func(p2)-fx;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-       p2[theta]=x[theta]-delt;
+         for (j=1;j<=nlstate+ndeath;j++){
-       k2=func(p2)-fx;
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+         }
+       for(d=0; d<dh[mi][i]; d++){
- #ifdef DEBUG
+         newm=savm;
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+         for (kk=1; kk<=cptcovage;kk++) {
- #endif
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+         }
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         k=kmax;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       }
+,nlstate+ndeath,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.;
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-       }
+         savm=oldm;
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+         oldm=newm;
-         delts=delt;
+       } /* end mult */
-       }
-     }
+       s1=s[mw[mi][i]][i];
-   }
+       s2=s[mw[mi+1][i]][i];
-   delti[theta]=delts;
+       bbh=(double)bh[mi][i]/(double)stepm;
-   return res;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
- }
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+         lli=log(out[s1][s2] - savm[s1][s2]);
- {
+       } else if  (s2==-2) {
-   int i;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   int l=1, l1, lmax=20;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   double k1,k2,k3,k4,res,fx;
+         lli= log(survp);
-   double p2[NPARMAX+1];
+       }else if (mle==1){
-   int k;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       } else if(mle==2){
-   fx=func(x);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   for (k=1; k<=2; k++) {
+       } else if(mle==3){  /* exponential inter-extrapolation */
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+         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 */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         lli=log(out[s1][s2]); /* Original formula */
-     k1=func(p2)-fx;
+       } else{  /* mle=0 back to 1 */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       } /* End of if */
-     k2=func(p2)-fx;
+       ipmx +=1;
+       sw += weight[i];
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-     k3=func(p2)-fx;
+       if(globpr){
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+  %11.6f %11.6f %11.6f ", \
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-     k4=func(p2)-fx;
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
- #ifdef DEBUG
+           llt +=ll[k]*gipmx/gsw;
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+         }
- #endif
+         fprintf(ficresilk," %10.6f\n", -llt);
-   }
+       }
-   return res;
+     } /* end of wave */
- }
+   } /* end of individual */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
- /************** Inverse of matrix **************/
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
- void ludcmp(double **a, int n, int *indx, double *d)
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
- {
+   if(globpr==0){ /* First time we count the contributions and weights */
-   int i,imax,j,k;
+     gipmx=ipmx;
-   double big,dum,sum,temp;
+     gsw=sw;
-   double *vv;
+   }
+   return -l;
-   vv=vector(1,n);
+ }
-   *d=1.0;
-   for (i=1;i<=n;i++) {
-     big=0.0;
+ /*************** function likelione ***********/
-     for (j=1;j<=n;j++)
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+ {
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+   /* This routine should help understanding what is done with
-     vv[i]=1.0/big;
+      the selection of individuals/waves and
-   }
+      to check the exact contribution to the likelihood.
-   for (j=1;j<=n;j++) {
+      Plotting could be done.
-     for (i=1;i<j;i++) {
+    */
-       sum=a[i][j];
+   int k;
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-       a[i][j]=sum;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     }
+     strcpy(fileresilk,"ilk");
-     big=0.0;
+     strcat(fileresilk,fileres);
-     for (i=j;i<=n;i++) {
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-       sum=a[i][j];
+       printf("Problem with resultfile: %s\n", fileresilk);
-       for (k=1;k<j;k++)
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-         sum -= a[i][k]*a[k][j];
+     }
-       a[i][j]=sum;
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-         big=dum;
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-         imax=i;
+     for(k=1; k<=nlstate; k++)
-       }
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-     }
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-     if (j != imax) {
+   }
-       for (k=1;k<=n;k++) {
-         dum=a[imax][k];
+   *fretone=(*funcone)(p);
-         a[imax][k]=a[j][k];
+   if(*globpri !=0){
-         a[j][k]=dum;
+     fclose(ficresilk);
-       }
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-       *d = -(*d);
+     fflush(fichtm);
-       vv[imax]=vv[j];
+   }
-     }
+   return;
-     indx[j]=imax;
+ }
-     if (a[j][j] == 0.0) a[j][j]=TINY;
-     if (j != n) {
-       dum=1.0/(a[j][j]);
+ /*********** Maximum Likelihood Estimation ***************/
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-     }
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   }
+ {
-   free_vector(vv,1,n);  /* Doesn't work */
+   int i,j, iter=0;
- ;
+   double **xi;
- }
+   double fret;
+   double fretone; /* Only one call to likelihood */
- void lubksb(double **a, int n, int *indx, double b[])
+   /*  char filerespow[FILENAMELENGTH];*/
- {
-   int i,ii=0,ip,j;
+ #ifdef NLOPT
-   double sum;
+   int creturn;
+   nlopt_opt opt;
-   for (i=1;i<=n;i++) {
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-     ip=indx[i];
+   double *lb;
-     sum=b[ip];
+   double minf; /* the minimum objective value, upon return */
-     b[ip]=b[i];
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-     if (ii)
+   myfunc_data dinst, *d = &dinst;
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+ #endif
-     else if (sum) ii=i;
-     b[i]=sum;
-   }
+   xi=matrix(1,npar,1,npar);
-   for (i=n;i>=1;i--) {
+   for (i=1;i<=npar;i++)
-     sum=b[i];
+     for (j=1;j<=npar;j++)
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     b[i]=sum/a[i][i];
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   }
+   strcpy(filerespow,"pow");
- }
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
- void pstamp(FILE *fichier)
+     printf("Problem with resultfile: %s\n", filerespow);
- {
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   }
- }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   for (i=1;i<=nlstate;i++)
- /************ Frequencies ********************/
+     for(j=1;j<=nlstate+ndeath;j++)
- 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[])
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- {  /* Some frequencies */
+   fprintf(ficrespow,"\n");
+ #ifdef POWELL
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-   int first;
+ #endif
-   double ***freq; /* Frequencies */
-   double *pp, **prop;
+ #ifdef NLOPT
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+ #ifdef NEWUOA
-   char fileresp[FILENAMELENGTH];
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
-   pp=vector(1,nlstate);
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+ #endif
-   strcpy(fileresp,"p");
+   lb=vector(0,npar-1);
-   strcat(fileresp,fileres);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   nlopt_set_lower_bounds(opt, lb);
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   nlopt_set_initial_step1(opt, 0.1);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-     exit(0);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   }
+   d->function = func;
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   j1=0;
+   nlopt_set_min_objective(opt, myfunc, d);
+   nlopt_set_xtol_rel(opt, ftol);
-   j=cptcoveff;
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+     printf("nlopt failed! %d\n",creturn);
+   }
-   first=1;
+   else {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   for(k1=1; k1<=j;k1++){
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     iter=1; /* not equal */
-       j1++;
+   }
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   nlopt_destroy(opt);
-         scanf("%d", i);*/
+ #endif
-       for (i=-5; i<=nlstate+ndeath; i++)
+   free_matrix(xi,1,npar,1,npar);
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   fclose(ficrespow);
-           for(m=iagemin; m <= iagemax+3; m++)
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-             freq[i][jk][m]=0;
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     for (i=1; i<=nlstate; i++)
-       for(m=iagemin; m <= iagemax+3; m++)
+ }
-         prop[i][m]=0;
+ /**** Computes Hessian and covariance matrix ***/
-       dateintsum=0;
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-       k2cpt=0;
+ {
-       for (i=1; i<=imx; i++) {
+   double  **a,**y,*x,pd;
-         bool=1;
+   double **hess;
-         if  (cptcovn>0) {
+   int i, j;
-           for (z1=1; z1<=cptcoveff; z1++)
+   int *indx;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-         }
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-         if (bool==1){
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-           for(m=firstpass; m<=lastpass; m++){
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-             k2=anint[m][i]+(mint[m][i]/12.);
+   double gompertz(double p[]);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+   hess=matrix(1,npar,1,npar);
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-               if (m<lastpass) {
+   for (i=1;i<=npar;i++){
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     printf("%d",i);fflush(stdout);
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-               }
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-                 dateintsum=dateintsum+k2;
+     /*  printf(" %f ",p[i]);
-                 k2cpt++;
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-               }
+   }
-               /*}*/
-           }
+   for (i=1;i<=npar;i++) {
-         }
+     for (j=1;j<=npar;j++)  {
-       }
+       if (j>i) {
+         printf(".%d%d",i,j);fflush(stdout);
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-       pstamp(ficresp);
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-       if  (cptcovn>0) {
-         fprintf(ficresp, "\n#********** Variable ");
+         hess[j][i]=hess[i][j];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         /*printf(" %lf ",hess[i][j]);*/
-         fprintf(ficresp, "**********\n#");
+       }
-       }
+     }
-       for(i=1; i<=nlstate;i++)
+   }
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   printf("\n");
-       fprintf(ficresp, "\n");
+   fprintf(ficlog,"\n");
-       for(i=iagemin; i <= iagemax+3; i++){
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-         if(i==iagemax+3){
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-           fprintf(ficlog,"Total");
-         }else{
+   a=matrix(1,npar,1,npar);
-           if(first==1){
+   y=matrix(1,npar,1,npar);
-             first=0;
+   x=vector(1,npar);
-             printf("See log file for details...\n");
+   indx=ivector(1,npar);
-           }
+   for (i=1;i<=npar;i++)
-           fprintf(ficlog,"Age %d", i);
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-         }
+   ludcmp(a,npar,indx,&pd);
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   for (j=1;j<=npar;j++) {
-             pp[jk] += freq[jk][m][i];
+     for (i=1;i<=npar;i++) x[i]=0;
-         }
+     x[j]=1;
-         for(jk=1; jk <=nlstate ; jk++){
+     lubksb(a,npar,indx,x);
-           for(m=-1, pos=0; m <=0 ; m++)
+     for (i=1;i<=npar;i++){
-             pos += freq[jk][m][i];
+       matcov[i][j]=x[i];
-           if(pp[jk]>=1.e-10){
+     }
-             if(first==1){
+   }
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             }
+   printf("\n#Hessian matrix#\n");
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-           }else{
+   for (i=1;i<=npar;i++) {
-             if(first==1)
+     for (j=1;j<=npar;j++) {
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       printf("%.3e ",hess[i][j]);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-           }
+     }
-         }
+     printf("\n");
+     fprintf(ficlog,"\n");
-         for(jk=1; jk <=nlstate ; jk++){
+   }
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
+   /* Recompute Inverse */
-         }
+   for (i=1;i<=npar;i++)
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-           pos += pp[jk];
+   ludcmp(a,npar,indx,&pd);
-           posprop += prop[jk][i];
-         }
+   /*  printf("\n#Hessian matrix recomputed#\n");
-         for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
+   for (j=1;j<=npar;j++) {
-             if(first==1)
+     for (i=1;i<=npar;i++) x[i]=0;
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     x[j]=1;
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     lubksb(a,npar,indx,x);
-           }else{
+     for (i=1;i<=npar;i++){
-             if(first==1)
+       y[i][j]=x[i];
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+       printf("%.3e ",y[i][j]);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+       fprintf(ficlog,"%.3e ",y[i][j]);
-           }
+     }
-           if( i <= iagemax){
+     printf("\n");
-             if(pos>=1.e-5){
+     fprintf(ficlog,"\n");
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   }
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+   */
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-             }
+   free_matrix(a,1,npar,1,npar);
-             else
+   free_matrix(y,1,npar,1,npar);
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   free_vector(x,1,npar);
-           }
+   free_ivector(indx,1,npar);
-         }
+   free_matrix(hess,1,npar,1,npar);
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
-           for(m=-1; m <=nlstate+ndeath; m++)
+ }
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+ /*************** hessian matrix ****************/
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+ {
-             }
+   int i;
-         if(i <= iagemax)
+   int l=1, lmax=20;
-           fprintf(ficresp,"\n");
+   double k1,k2;
-         if(first==1)
+   double p2[MAXPARM+1]; /* identical to x */
-           printf("Others in log...\n");
+   double res;
-         fprintf(ficlog,"\n");
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-       }
+   double fx;
-     }
+   int k=0,kmax=10;
-   }
+   double l1;
-   dateintmean=dateintsum/k2cpt;
+   fx=func(x);
-   fclose(ficresp);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   free_vector(pp,1,nlstate);
+     l1=pow(10,l);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+     delts=delt;
-   /* End of Freq */
+     for(k=1 ; k <kmax; k=k+1){
- }
+       delt = delta*(l1*k);
+       p2[theta]=x[theta] +delt;
- /************ Prevalence ********************/
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
- 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;
- {
+       k2=func(p2)-fx;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-      We still use firstpass and lastpass as another selection.
-   */
+ #ifdef DEBUGHESS
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+       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 ***freq; /* Frequencies */
+ #endif
-   double *pp, **prop;
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   double pos,posprop;
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   double  y2; /* in fractional years */
+         k=kmax;
-   int iagemin, iagemax;
+       }
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   iagemin= (int) agemin;
+         k=kmax; l=lmax*10;
-   iagemax= (int) agemax;
+       }
-   /*pp=vector(1,nlstate);*/
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         delts=delt;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+       }
-   j1=0;
+     }
+   }
-   j=cptcoveff;
+   delti[theta]=delts;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   return res;
-   for(k1=1; k1<=j;k1++){
+ }
-     for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ {
-       for (i=1; i<=nlstate; i++)
+   int i;
-         for(m=iagemin; m <= iagemax+3; m++)
+   int l=1, lmax=20;
-           prop[i][m]=0.0;
+   double k1,k2,k3,k4,res,fx;
+   double p2[MAXPARM+1];
-       for (i=1; i<=imx; i++) { /* Each individual */
+   int k;
-         bool=1;
-         if  (cptcovn>0) {
+   fx=func(x);
-           for (z1=1; z1<=cptcoveff; z1++)
+   for (k=1; k<=2; k++) {
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-               bool=0;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-         }
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-         if (bool==1) {
+     k1=func(p2)-fx;
-           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 */
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     k2=func(p2)-fx;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+     k3=func(p2)-fx;
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-                 prop[s[m][i]][iagemax+3] += weight[i];
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-               }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-             }
+     k4=func(p2)-fx;
-           } /* end selection of waves */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-         }
+ #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(i=iagemin; i <= iagemax+3; i++){
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ #endif
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+   }
-           posprop += prop[jk][i];
+   return res;
-         }
+ }
-         for(jk=1; jk <=nlstate ; jk++){
+ /************** Inverse of matrix **************/
-           if( i <=  iagemax){
+ void ludcmp(double **a, int n, int *indx, double *d)
-             if(posprop>=1.e-5){
+ {
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+   int i,imax,j,k;
-             }
+   double big,dum,sum,temp;
-           }
+   double *vv;
-         }/* end jk */
-       }/* end i */
+   vv=vector(1,n);
-     } /* end i1 */
+   *d=1.0;
-   } /* end k1 */
+   for (i=1;i<=n;i++) {
+     big=0.0;
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+     for (j=1;j<=n;j++)
-   /*free_vector(pp,1,nlstate);*/
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
- }  /* End of prevalence */
+     vv[i]=1.0/big;
+   }
- /************* Waves Concatenation ***************/
+   for (j=1;j<=n;j++) {
+     for (i=1;i<j;i++) {
- 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)
+       sum=a[i][j];
- {
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       a[i][j]=sum;
-      Death is a valid wave (if date is known).
+     }
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+     big=0.0;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+     for (i=j;i<=n;i++) {
-      and mw[mi+1][i]. dh depends on stepm.
+       sum=a[i][j];
-      */
+       for (k=1;k<j;k++)
+         sum -= a[i][k]*a[k][j];
-   int i, mi, m;
+       a[i][j]=sum;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-      double sum=0., jmean=0.;*/
+         big=dum;
-   int first;
+         imax=i;
-   int j, k=0,jk, ju, jl;
+       }
-   double sum=0.;
+     }
-   first=0;
+     if (j != imax) {
-   jmin=1e+5;
+       for (k=1;k<=n;k++) {
-   jmax=-1;
+         dum=a[imax][k];
-   jmean=0.;
+         a[imax][k]=a[j][k];
-   for(i=1; i<=imx; i++){
+         a[j][k]=dum;
-     mi=0;
+       }
-     m=firstpass;
+       *d = -(*d);
-     while(s[m][i] <= nlstate){
+       vv[imax]=vv[j];
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+     }
-         mw[++mi][i]=m;
+     indx[j]=imax;
-       if(m >=lastpass)
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-         break;
+     if (j != n) {
-       else
+       dum=1.0/(a[j][j]);
-         m++;
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-     }/* end while */
+     }
-     if (s[m][i] > nlstate){
+   }
-       mi++;     /* Death is another wave */
+   free_vector(vv,1,n);  /* Doesn't work */
-       /* if(mi==0)  never been interviewed correctly before death */
+ ;
-          /* Only death is a correct wave */
+ }
-       mw[mi][i]=m;
-     }
+ void lubksb(double **a, int n, int *indx, double b[])
+ {
-     wav[i]=mi;
+   int i,ii=0,ip,j;
-     if(mi==0){
+   double sum;
-       nbwarn++;
-       if(first==0){
+   for (i=1;i<=n;i++) {
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+     ip=indx[i];
-         first=1;
+     sum=b[ip];
-       }
+     b[ip]=b[i];
-       if(first==1){
+     if (ii)
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-       }
+     else if (sum) ii=i;
-     } /* end mi==0 */
+     b[i]=sum;
-   } /* End individuals */
+   }
+   for (i=n;i>=1;i--) {
-   for(i=1; i<=imx; i++){
+     sum=b[i];
-     for(mi=1; mi<wav[i];mi++){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       if (stepm <=0)
+     b[i]=sum/a[i][i];
-         dh[mi][i]=1;
+   }
-       else{
+ }
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-           if (agedc[i] < 2*AGESUP) {
+ void pstamp(FILE *fichier)
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+ {
-             if(j==0) j=1;  /* Survives at least one month after exam */
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-             else if(j<0){
+ }
-               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]);
+ /************ Frequencies ********************/
-               j=1; /* Temporary Dangerous patch */
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-               printf("   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 */
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   int i, m, jk, j1, bool, z1,j;
-             }
+   int first;
-             k=k+1;
+   double ***freq; /* Frequencies */
-             if (j >= jmax){
+   double *pp, **prop;
-               jmax=j;
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-               ijmax=i;
+   char fileresp[FILENAMELENGTH];
-             }
-             if (j <= jmin){
+   pp=vector(1,nlstate);
-               jmin=j;
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-               ijmin=i;
+   strcpy(fileresp,"p");
-             }
+   strcat(fileresp,fileres);
-             sum=sum+j;
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-           }
+     exit(0);
-         }
+   }
-         else{
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   j1=0;
- /*        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]); */
+   j=cptcoveff;
-           k=k+1;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           if (j >= jmax) {
-             jmax=j;
+   first=1;
-             ijmax=i;
-           }
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-           else if (j <= jmin){
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
-             jmin=j;
+   /*    j1++; */
-             ijmin=i;
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-           }
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+         scanf("%d", 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 (i=-5; i<=nlstate+ndeath; i++)
-           if(j<0){
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-             nberr++;
+           for(m=iagemin; m <= iagemax+3; m++)
-             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]);
+             freq[i][jk][m]=0;
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           }
+       for (i=1; i<=nlstate; i++)
-           sum=sum+j;
+         for(m=iagemin; m <= iagemax+3; m++)
-         }
+           prop[i][m]=0;
-         jk= j/stepm;
-         jl= j -jk*stepm;
+       dateintsum=0;
-         ju= j -(jk+1)*stepm;
+       k2cpt=0;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+       for (i=1; i<=imx; i++) {
-           if(jl==0){
+         bool=1;
-             dh[mi][i]=jk;
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-             bh[mi][i]=0;
+           for (z1=1; z1<=cptcoveff; z1++)
-           }else{ /* We want a negative bias in order to only have interpolation ie
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-                   * at the price of an extra matrix product in likelihood */
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-             dh[mi][i]=jk+1;
+               bool=0;
-             bh[mi][i]=ju;
+               /* 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",
-           }
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-         }else{
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-           if(jl <= -ju){
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-             dh[mi][i]=jk;
+             }
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         }
-                                  * is higher than the multiple of stepm and negative otherwise.
-                                  */
+         if (bool==1){
-           }
+           for(m=firstpass; m<=lastpass; m++){
-           else{
+             k2=anint[m][i]+(mint[m][i]/12.);
-             dh[mi][i]=jk+1;
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-             bh[mi][i]=ju;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-           }
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-           if(dh[mi][i]==0){
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-             dh[mi][i]=1; /* At least one step */
+               if (m<lastpass) {
-             bh[mi][i]=ju; /* At least one step */
+                 freq[s[m][i]][s[m+1][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);*/
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-           }
+               }
-         } /* end if mle */
-       }
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-     } /* end wave */
+                 dateintsum=dateintsum+k2;
-   }
+                 k2cpt++;
-   jmean=sum/k;
+               }
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+               /*}*/
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+           }
-  }
+         }
+       } /* end i */
- /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx)
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- {
+       pstamp(ficresp);
+       if  (cptcovn>0) {
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+         fprintf(ficresp, "\n#********** Variable ");
-   int cptcode=0;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   cptcoveff=0;
+         fprintf(ficresp, "**********\n#");
+         fprintf(ficlog, "\n#********** Variable ");
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+         fprintf(ficlog, "**********\n#");
+       }
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+       for(i=1; i<=nlstate;i++)
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-                                modality*/
+       fprintf(ficresp, "\n");
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
-       Ndum[ij]++; /*store the modality */
+       for(i=iagemin; i <= iagemax+3; i++){
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+         if(i==iagemax+3){
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+           fprintf(ficlog,"Total");
-                                        Tvar[j]. If V=sex and male is 0 and
+         }else{
-                                        female is 1, then  cptcode=1.*/
+           if(first==1){
-     }
+             first=0;
+             printf("See log file for details...\n");
-     for (i=0; i<=cptcode; i++) {
+           }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+           fprintf(ficlog,"Age %d", i);
-     }
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-     ij=1;
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-     for (i=1; i<=ncodemax[j]; i++) {
+             pp[jk] += freq[jk][m][i];
-       for (k=0; k<= maxncov; k++) {
+         }
-         if (Ndum[k] != 0) {
+         for(jk=1; jk <=nlstate ; jk++){
-           nbcode[Tvar[j]][ij]=k;
+           for(m=-1, pos=0; m <=0 ; m++)
-           /* 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; */
+             pos += freq[jk][m][i];
+           if(pp[jk]>=1.e-10){
-           ij++;
+             if(first==1){
-         }
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-         if (ij > ncodemax[j]) break;
+             }
-       }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-     }
+           }else{
-   }
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
-  for (i=1; i<=ncovmodel-2; i++) {
+         }
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-    ij=Tvar[i];
+         for(jk=1; jk <=nlstate ; jk++){
-    Ndum[ij]++;
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-  }
+             pp[jk] += freq[jk][m][i];
+         }
-  ij=1;
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-  for (i=1; i<= maxncov; i++) {
+           pos += pp[jk];
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+           posprop += prop[jk][i];
-      Tvaraff[ij]=i; /*For printing */
+         }
-      ij++;
+         for(jk=1; jk <=nlstate ; jk++){
-    }
+           if(pos>=1.e-5){
-  }
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-  cptcoveff=ij-1; /*Number of simple covariates*/
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- }
+           }else{
+             if(first==1)
- /*********** Health Expectancies ****************/
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- 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[] )
+           }
+           if( i <= iagemax){
- {
+             if(pos>=1.e-5){
-   /* Health expectancies, no variances */
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   double age, agelim, hf;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   double ***p3mat;
+             }
-   double eip;
+             else
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-   pstamp(ficreseij);
+           }
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+         }
-   fprintf(ficreseij,"# Age");
-   for(i=1; i<=nlstate;i++){
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-     for(j=1; j<=nlstate;j++){
+           for(m=-1; m <=nlstate+ndeath; m++)
-       fprintf(ficreseij," e%1d%1d ",i,j);
+             if(freq[jk][m][i] !=0 ) {
-     }
+             if(first==1)
-     fprintf(ficreseij," e%1d. ",i);
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   }
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   fprintf(ficreseij,"\n");
+             }
+         if(i <= iagemax)
+           fprintf(ficresp,"\n");
-   if(estepm < stepm){
+         if(first==1)
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+           printf("Others in log...\n");
-   }
+         fprintf(ficlog,"\n");
-   else  hstepm=estepm;
+       }
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       /*}*/
-    * This is mainly to measure the difference between two models: for example
+   }
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   dateintmean=dateintsum/k2cpt;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
-    * progression in between and thus overestimating or underestimating according
+   fclose(ficresp);
-    * to the curvature of the survival function. If, for the same date, we
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   free_vector(pp,1,nlstate);
-    * to compare the new estimate of Life expectancy with the same linear
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-    * hypothesis. A more precise result, taking into account a more precise
+   /* End of Freq */
-    * curvature will be obtained if estepm is as small as stepm. */
+ }
-   /* For example we decided to compute the life expectancy with the smallest unit */
+ /************ Prevalence ********************/
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+ 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)
-      nhstepm is the number of hstepm from age to agelim
+ {
-      nstepm is the number of stepm from age to agelin.
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-      Look at hpijx to understand the reason of that which relies in memory size
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-      and note for a fixed period like estepm months */
+      We still use firstpass and lastpass as another selection.
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   */
-      survival function given by stepm (the optimization length). Unfortunately it
-      means that if the survival funtion is printed only each two years of age and if
+   int i, m, jk, j1, bool, z1,j;
-      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.
+   double **prop;
-   */
+   double posprop;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   double  y2; /* in fractional years */
+   int iagemin, iagemax;
-   agelim=AGESUP;
+   int first; /** to stop verbosity which is redirected to log file */
-   /* If stepm=6 months */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+   iagemin= (int) agemin;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   iagemax= (int) agemax;
+   /*pp=vector(1,nlstate);*/
- /* nhstepm age range expressed in number of stepm */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   j1=0;
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   /*j=cptcoveff;*/
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   for (age=bage; age<=fage; age ++){
+   first=1;
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       j1++;*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       for (i=1; i<=nlstate; i++)
+         for(m=iagemin; m <= iagemax+3; m++)
-     printf("%d|",(int)age);fflush(stdout);
+           prop[i][m]=0.0;
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+       for (i=1; i<=imx; i++) { /* Each individual */
+         bool=1;
-     /* Computing expectancies */
+         if  (cptcovn>0) {
-     for(i=1; i<=nlstate;i++)
+           for (z1=1; z1<=cptcoveff; z1++)
-       for(j=1; j<=nlstate;j++)
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+               bool=0;
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+         }
+         if (bool==1) {
-           /*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(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 */
-         }
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-     fprintf(ficreseij,"%3.0f",age );
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-     for(i=1; i<=nlstate;i++){
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-       eip=0;
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-       for(j=1; j<=nlstate;j++){
+                 /*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]]);*/
-         eip +=eij[i][j][(int)age];
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+                 prop[s[m][i]][iagemax+3] += weight[i];
-       }
+               }
-       fprintf(ficreseij,"%9.4f", eip );
+             }
-     }
+           } /* end selection of waves */
-     fprintf(ficreseij,"\n");
+         }
+       }
-   }
+       for(i=iagemin; i <= iagemax+3; i++){
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   printf("\n");
+           posprop += prop[jk][i];
-   fprintf(ficlog,"\n");
+         }
- }
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <=  iagemax){
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
- {
+             } else{
-   /* Covariances of health expectancies eij and of total life expectancies according
+               if(first==1){
-    to initial status i, ei. .
+                 first=0;
-   */
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+               }
-   double age, agelim, hf;
+             }
-   double ***p3matp, ***p3matm, ***varhe;
+           }
-   double **dnewm,**doldm;
+         }/* end jk */
-   double *xp, *xm;
+       }/* end i */
-   double **gp, **gm;
+     /*} *//* end i1 */
-   double ***gradg, ***trgradg;
+   } /* end j1 */
-   int theta;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   double eip, vip;
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+ }  /* End of prevalence */
-   xp=vector(1,npar);
-   xm=vector(1,npar);
+ /************* Waves Concatenation ***************/
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+ 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)
+ {
-   pstamp(ficresstdeij);
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+      Death is a valid wave (if date is known).
-   fprintf(ficresstdeij,"# Age");
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-   for(i=1; i<=nlstate;i++){
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-     for(j=1; j<=nlstate;j++)
+      and mw[mi+1][i]. dh depends on stepm.
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+      */
-     fprintf(ficresstdeij," e%1d. ",i);
-   }
+   int i, mi, m;
-   fprintf(ficresstdeij,"\n");
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+      double sum=0., jmean=0.;*/
-   pstamp(ficrescveij);
+   int first;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   int j, k=0,jk, ju, jl;
-   fprintf(ficrescveij,"# Age");
+   double sum=0.;
-   for(i=1; i<=nlstate;i++)
+   first=0;
-     for(j=1; j<=nlstate;j++){
+   jmin=100000;
-       cptj= (j-1)*nlstate+i;
+   jmax=-1;
-       for(i2=1; i2<=nlstate;i2++)
+   jmean=0.;
-         for(j2=1; j2<=nlstate;j2++){
+   for(i=1; i<=imx; i++){
-           cptj2= (j2-1)*nlstate+i2;
+     mi=0;
-           if(cptj2 <= cptj)
+     m=firstpass;
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+     while(s[m][i] <= nlstate){
-         }
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-     }
+         mw[++mi][i]=m;
-   fprintf(ficrescveij,"\n");
+       if(m >=lastpass)
+         break;
-   if(estepm < stepm){
+       else
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         m++;
-   }
+     }/* end while */
-   else  hstepm=estepm;
+     if (s[m][i] > nlstate){
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       mi++;     /* Death is another wave */
-    * This is mainly to measure the difference between two models: for example
+       /* if(mi==0)  never been interviewed correctly before death */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+          /* Only death is a correct wave */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       mw[mi][i]=m;
-    * progression in between and thus overestimating or underestimating according
+     }
-    * 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
+     wav[i]=mi;
-    * to compare the new estimate of Life expectancy with the same linear
+     if(mi==0){
-    * hypothesis. A more precise result, taking into account a more precise
+       nbwarn++;
-    * curvature will be obtained if estepm is as small as stepm. */
+       if(first==0){
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+         first=1;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       }
-      nhstepm is the number of hstepm from age to agelim
+       if(first==1){
-      nstepm is the number of stepm from age to agelin.
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-      Look at hpijx to understand the reason of that which relies in memory size
+       }
-      and note for a fixed period like estepm months */
+     } /* end mi==0 */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   } /* End individuals */
-      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
+   for(i=1; i<=imx; i++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     for(mi=1; mi<wav[i];mi++){
-      results. So we changed our mind and took the option of the best precision.
+       if (stepm <=0)
-   */
+         dh[mi][i]=1;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       else{
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-   /* If stepm=6 months */
+           if (agedc[i] < 2*AGESUP) {
-   /* nhstepm age range expressed in number of stepm */
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-   agelim=AGESUP;
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+             else if(j<0){
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+               nberr++;
-   /* if (stepm >= YEARM) hstepm=1;*/
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+               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);
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               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]);
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               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);
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+             }
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+             k=k+1;
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+             if (j >= jmax){
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+               jmax=j;
+               ijmax=i;
-   for (age=bage; age<=fage; age ++){
+             }
+             if (j <= jmin){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+               jmin=j;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+               ijmin=i;
+             }
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             sum=sum+j;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-     /* Computing  Variances of health expectancies */
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+           }
-        decrease memory allocation */
+         }
-     for(theta=1; theta <=npar; theta++){
+         else{
-       for(i=1; i<=npar; i++){
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ /*        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]); */
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-       }
+           k=k+1;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+           if (j >= jmax) {
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+             jmax=j;
+             ijmax=i;
-       for(j=1; j<= nlstate; j++){
+           }
-         for(i=1; i<=nlstate; i++){
+           else if (j <= jmin){
-           for(h=0; h<=nhstepm-1; h++){
+             jmin=j;
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             ijmin=i;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+           }
-           }
+           /*        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]);*/
-       }
+           if(j<0){
+             nberr++;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+             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(h=0; h<=nhstepm-1; h++){
+             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]);
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+           }
-         }
+           sum=sum+j;
-     }/* End theta */
+         }
+         jk= j/stepm;
+         jl= j -jk*stepm;
-     for(h=0; h<=nhstepm-1; h++)
+         ju= j -(jk+1)*stepm;
-       for(j=1; j<=nlstate*nlstate;j++)
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-         for(theta=1; theta <=npar; theta++)
+           if(jl==0){
-           trgradg[h][j][theta]=gradg[h][theta][j];
+             dh[mi][i]=jk;
+             bh[mi][i]=0;
+           }else{ /* We want a negative bias in order to only have interpolation ie
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+                   * to avoid the price of an extra matrix product in likelihood */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+             dh[mi][i]=jk+1;
-         varhe[ij][ji][(int)age] =0.;
+             bh[mi][i]=ju;
+           }
-      printf("%d|",(int)age);fflush(stdout);
+         }else{
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           if(jl <= -ju){
-      for(h=0;h<=nhstepm-1;h++){
+             dh[mi][i]=jk;
-       for(k=0;k<=nhstepm-1;k++){
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+                                  * is higher than the multiple of stepm and negative otherwise.
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+                                  */
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+           }
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+           else{
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+             dh[mi][i]=jk+1;
-       }
+             bh[mi][i]=ju;
-     }
+           }
+           if(dh[mi][i]==0){
-     /* Computing expectancies */
+             dh[mi][i]=1; /* At least one step */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+             bh[mi][i]=ju; /* At least one step */
-     for(i=1; i<=nlstate;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);*/
-       for(j=1; j<=nlstate;j++)
+           }
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+         } /* end if mle */
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+       }
+     } /* end wave */
-           /* 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]);*/
+   }
+   jmean=sum/k;
-         }
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-     fprintf(ficresstdeij,"%3.0f",age );
+  }
-     for(i=1; i<=nlstate;i++){
-       eip=0.;
+ /*********** Tricode ****************************/
-       vip=0.;
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-       for(j=1; j<=nlstate;j++){
+ {
-         eip += eij[i][j][(int)age];
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-       }
+    * nbcode[Tvar[j]][1]=
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+   */
-     }
-     fprintf(ficresstdeij,"\n");
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
-     fprintf(ficrescveij,"%3.0f",age );
+   int cptcode=0; /* Modality max of covariates j */
-     for(i=1; i<=nlstate;i++)
+   int modmincovj=0; /* Modality min of covariates j */
-       for(j=1; j<=nlstate;j++){
-         cptj= (j-1)*nlstate+i;
-         for(i2=1; i2<=nlstate;i2++)
+   cptcoveff=0;
-           for(j2=1; j2<=nlstate;j2++){
-             cptj2= (j2-1)*nlstate+i2;
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-             if(cptj2 <= cptj)
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-           }
+   /* Loop on covariates without age and products */
-       }
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-     fprintf(ficrescveij,"\n");
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
+                                modality of this covariate Vj*/
-   }
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+                                     * If product of Vn*Vm, still boolean *:
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                       modality of the nth covariate of individual i. */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       if (ij > modmaxcovj)
-   printf("\n");
+         modmaxcovj=ij;
-   fprintf(ficlog,"\n");
+       else if (ij < modmincovj)
+         modmincovj=ij;
-   free_vector(xm,1,npar);
+       if ((ij < -1) && (ij > NCOVMAX)){
-   free_vector(xp,1,npar);
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+         exit(1);
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+       }else
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
- }
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
- /************ Variance ******************/
+       /* getting the maximum value of the modality of the covariate
- 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[])
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
- {
+          female is 1, then modmaxcovj=1.*/
-   /* Variance of health expectancies */
+     }
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   /* double **newm;*/
+     cptcode=modmaxcovj;
-   double **dnewm,**doldm;
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   double **dnewmp,**doldmp;
+    /*for (i=0; i<=cptcode; i++) {*/
-   int i, j, nhstepm, hstepm, h, nstepm ;
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-   int k, cptcode;
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-   double *xp;
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-   double **gp, **gm;  /* for var eij */
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-   double ***gradg, ***trgradg; /*for var eij */
+       }
-   double **gradgp, **trgradgp; /* for var p point j */
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   double *gpp, *gmp; /* for var p point j */
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+     } /* Ndum[-1] number of undefined modalities */
-   double ***p3mat;
-   double age,agelim, hf;
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-   double ***mobaverage;
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-   int theta;
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-   char digit[4];
+        modmincovj=3; modmaxcovj = 7;
-   char digitp[25];
+        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
-   char fileresprobmorprev[FILENAMELENGTH];
+        variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
-   if(popbased==1){
+        nbcode[Tvar[j]][1]=0;
-     if(mobilav!=0)
+        nbcode[Tvar[j]][2]=1;
-       strcpy(digitp,"-populbased-mobilav-");
+        nbcode[Tvar[j]][3]=2;
-     else strcpy(digitp,"-populbased-nomobil-");
+     */
-   }
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   else
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-     strcpy(digitp,"-stablbased-");
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+         /*recode from 0 */
-   if (mobilav!=0) {
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+                                      k is a modality. If we have model=V1+V1*sex
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+           ij++;
-     }
+         }
-   }
+         if (ij > ncodemax[j]) break;
+       }  /* end of loop on */
-   strcpy(fileresprobmorprev,"prmorprev");
+     } /* end of loop on modality */
-   sprintf(digit,"%-d",ij);
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    Ndum[ij]++;
-   }
+  }
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  ij=1;
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-   pstamp(ficresprobmorprev);
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   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);
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      Tvaraff[ij]=i; /*For printing (unclear) */
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+      ij++;
-     for(i=1; i<=nlstate;i++)
+    }else
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+        Tvaraff[ij]=0;
-   }
+  }
-   fprintf(ficresprobmorprev,"\n");
+  ij--;
-   fprintf(ficgp,"\n# Routine varevsij");
+  cptcoveff=ij; /*Number of total covariates*/
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+ }
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ /*********** Health Expectancies ****************/
-   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+ {
-   else
+   /* Health expectancies, no variances */
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   int i, j, nhstepm, hstepm, h, nstepm;
-   fprintf(ficresvij,"# Age");
+   int nhstepma, nstepma; /* Decreasing with age */
-   for(i=1; i<=nlstate;i++)
+   double age, agelim, hf;
-     for(j=1; j<=nlstate;j++)
+   double ***p3mat;
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   double eip;
-   fprintf(ficresvij,"\n");
+   pstamp(ficreseij);
-   xp=vector(1,npar);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   dnewm=matrix(1,nlstate,1,npar);
+   fprintf(ficreseij,"# Age");
-   doldm=matrix(1,nlstate,1,nlstate);
+   for(i=1; i<=nlstate;i++){
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+     for(j=1; j<=nlstate;j++){
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+     fprintf(ficreseij," e%1d. ",i);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   }
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   fprintf(ficreseij,"\n");
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
    else  hstepm=estepm;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+    * This is mainly to measure the difference between two models: for example
-      nhstepm is the number of hstepm from age to agelim
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-      nstepm is the number of stepm from age to agelin.
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-      Look at hpijx to understand the reason of that which relies in memory size
+    * progression in between and thus overestimating or underestimating according
-      and note for a fixed period like k years */
+    * to the curvature of the survival function. If, for the same date, we
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-      survival function given by stepm (the optimization length). Unfortunately it
+    * to compare the new estimate of Life expectancy with the same linear
-      means that if the survival funtion is printed every two years of age and if
+    * hypothesis. A more precise result, taking into account a more precise
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+    * curvature will be obtained if estepm is as small as stepm. */
-      results. So we changed our mind and took the option of the best precision.
-   */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   agelim = AGESUP;
+      nhstepm is the number of hstepm from age to agelim
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+      nstepm is the number of stepm from age to agelin.
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+      Look at hpijx to understand the reason of that which relies in memory size
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      and note for a fixed period like estepm months */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+      survival function given by stepm (the optimization length). Unfortunately it
-     gp=matrix(0,nhstepm,1,nlstate);
+      means that if the survival funtion is printed only each two years of age and if
-     gm=matrix(0,nhstepm,1,nlstate);
+      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(theta=1; theta <=npar; theta++){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   agelim=AGESUP;
-       }
+   /* If stepm=6 months */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-       if (popbased==1) {
+ /* nhstepm age range expressed in number of stepm */
-         if(mobilav ==0){
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-           for(i=1; i<=nlstate;i++)
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-             prlim[i][i]=probs[(int)age][i][ij];
+   /* if (stepm >= YEARM) hstepm=1;*/
-         }else{ /* mobilav */
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           for(i=1; i<=nlstate;i++)
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+   for (age=bage; age<=fage; age ++){
-       }
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(j=1; j<= nlstate; j++){
+     /* if (stepm >= YEARM) hstepm=1;*/
-         for(h=0; h<=nhstepm; h++){
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+     /* If stepm=6 months */
-         }
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-       }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-          as a weighted average of prlim.
-       */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+     printf("%d|",(int)age);fflush(stdout);
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       }
-       /* end probability of death */
+     /* Computing expectancies */
+     for(i=1; i<=nlstate;i++)
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+       for(j=1; j<=nlstate;j++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+           /* 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 (popbased==1) {
-         if(mobilav ==0){
+         }
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+     fprintf(ficreseij,"%3.0f",age );
-         }else{ /* mobilav */
+     for(i=1; i<=nlstate;i++){
-           for(i=1; i<=nlstate;i++)
+       eip=0;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+       for(j=1; j<=nlstate;j++){
-         }
+         eip +=eij[i][j][(int)age];
-       }
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
-       for(j=1; j<= nlstate; j++){
+       fprintf(ficreseij,"%9.4f", eip );
-         for(h=0; h<=nhstepm; h++){
+     }
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+     fprintf(ficreseij,"\n");
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
+   }
-       }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       /* This for computing probability of death (h=1 means
+   printf("\n");
-          computed over hstepm matrices product = hstepm*stepm months)
+   fprintf(ficlog,"\n");
-          as a weighted average of prlim.
-       */
+ }
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+ 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[] )
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+ {
-       /* end probability of death */
+   /* Covariances of health expectancies eij and of total life expectancies according
+    to initial status i, ei. .
-       for(j=1; j<= nlstate; j++) /* vareij */
+   */
-         for(h=0; h<=nhstepm; h++){
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   int nhstepma, nstepma; /* Decreasing with age */
-         }
+   double age, agelim, hf;
+   double ***p3matp, ***p3matm, ***varhe;
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   double **dnewm,**doldm;
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   double *xp, *xm;
-       }
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
-     } /* End theta */
+   int theta;
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   double eip, vip;
-     for(h=0; h<=nhstepm; h++) /* veij */
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-       for(j=1; j<=nlstate;j++)
+   xp=vector(1,npar);
-         for(theta=1; theta <=npar; theta++)
+   xm=vector(1,npar);
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       for(theta=1; theta <=npar; theta++)
+   pstamp(ficresstdeij);
-         trgradgp[j][theta]=gradgp[theta][j];
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     for(j=1; j<=nlstate;j++)
-     for(i=1;i<=nlstate;i++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       for(j=1;j<=nlstate;j++)
+     fprintf(ficresstdeij," e%1d. ",i);
-         vareij[i][j][(int)age] =0.;
+   }
+   fprintf(ficresstdeij,"\n");
-     for(h=0;h<=nhstepm;h++){
-       for(k=0;k<=nhstepm;k++){
+   pstamp(ficrescveij);
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+   fprintf(ficrescveij,"# 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] += doldm[i][j]*hf*hf;
+       cptj= (j-1)*nlstate+i;
-       }
+       for(i2=1; i2<=nlstate;i2++)
-     }
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
-     /* pptj */
+           if(cptj2 <= cptj)
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+         }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+     }
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+   fprintf(ficrescveij,"\n");
-         varppt[j][i]=doldmp[j][i];
-     /* end ppptj */
+   if(estepm < stepm){
-     /*  x centered again */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   }
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     if (popbased==1) {
+    * This is mainly to measure the difference between two models: for example
-       if(mobilav ==0){
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-         for(i=1; i<=nlstate;i++)
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-           prlim[i][i]=probs[(int)age][i][ij];
+    * progression in between and thus overestimating or underestimating according
-       }else{ /* mobilav */
+    * to the curvature of the survival function. If, for the same date, we
-         for(i=1; i<=nlstate;i++)
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+    * to compare the new estimate of Life expectancy with the same linear
-       }
+    * hypothesis. A more precise result, taking into account a more precise
-     }
+    * curvature will be obtained if estepm is as small as stepm. */
-     /* This for computing probability of death (h=1 means
+   /* For example we decided to compute the life expectancy with the smallest unit */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-        as a weighted average of prlim.
+      nhstepm is the number of hstepm from age to agelim
-     */
+      nstepm is the number of stepm from age to agelin.
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+      Look at hpijx to understand the reason of that which relies in memory size
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+      and note for a fixed period like estepm months */
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   /* 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 probability of death */
+      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
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      results. So we changed our mind and took the option of the best precision.
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   /* If stepm=6 months */
-       }
+   /* nhstepm age range expressed in number of stepm */
-     }
+   agelim=AGESUP;
-     fprintf(ficresprobmorprev,"\n");
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     fprintf(ficresvij,"%.0f ",age );
+   /* if (stepm >= YEARM) hstepm=1;*/
-     for(i=1; i<=nlstate;i++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficresvij,"\n");
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_matrix(gp,0,nhstepm,1,nlstate);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){
-   } /* End age */
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+     /* if (stepm >= YEARM) hstepm=1;*/
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     /* If stepm=6 months */
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- /*   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));
+     /* Computing  Variances of health expectancies */
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+        decrease memory allocation */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+     for(theta=1; theta <=npar; theta++){
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       for(i=1; i<=npar; i++){
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
- */
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+       }
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+       for(j=1; j<= nlstate; j++){
-   free_matrix(dnewm,1,nlstate,1,npar);
+         for(i=1; i<=nlstate; i++){
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+           for(h=0; h<=nhstepm-1; h++){
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           }
-   fclose(ficresprobmorprev);
+         }
-   fflush(ficgp);
+       }
-   fflush(fichtm);
- }  /* end varevsij */
+       for(ij=1; ij<= nlstate*nlstate; ij++)
+         for(h=0; h<=nhstepm-1; h++){
- /************ Variance of prevlim ******************/
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- 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[])
+         }
- {
+     }/* End theta */
-   /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
+     for(h=0; h<=nhstepm-1; h++)
-   double **dnewm,**doldm;
+       for(j=1; j<=nlstate*nlstate;j++)
-   int i, j, nhstepm, hstepm;
+         for(theta=1; theta <=npar; theta++)
-   int k, cptcode;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   double *xp;
-   double *gp, *gm;
-   double **gradg, **trgradg;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   double age,agelim;
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   int theta;
+         varhe[ij][ji][(int)age] =0.;
-   pstamp(ficresvpl);
+      printf("%d|",(int)age);fflush(stdout);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   fprintf(ficresvpl,"# Age");
+      for(h=0;h<=nhstepm-1;h++){
-   for(i=1; i<=nlstate;i++)
+       for(k=0;k<=nhstepm-1;k++){
-       fprintf(ficresvpl," %1d-%1d",i,i);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-   fprintf(ficresvpl,"\n");
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   xp=vector(1,npar);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   dnewm=matrix(1,nlstate,1,npar);
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   doldm=matrix(1,nlstate,1,nlstate);
+       }
+     }
-   hstepm=1*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     /* Computing expectancies */
-   agelim = AGESUP;
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     for(i=1; i<=nlstate;i++)
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       for(j=1; j<=nlstate;j++)
-     if (stepm >= YEARM) hstepm=1;
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-     gradg=matrix(1,npar,1,nlstate);
-     gp=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]);*/
-     gm=vector(1,nlstate);
+         }
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     fprintf(ficresstdeij,"%3.0f",age );
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     for(i=1; i<=nlstate;i++){
-       }
+       eip=0.;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       vip=0.;
-       for(i=1;i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-         gp[i] = prlim[i][i];
+         eip += eij[i][j][(int)age];
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       for(i=1;i<=nlstate;i++)
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-         gm[i] = prlim[i][i];
+     }
+     fprintf(ficresstdeij,"\n");
-       for(i=1;i<=nlstate;i++)
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+     fprintf(ficrescveij,"%3.0f",age );
-     } /* End theta */
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-     trgradg =matrix(1,nlstate,1,npar);
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-     for(j=1; j<=nlstate;j++)
+           for(j2=1; j2<=nlstate;j2++){
-       for(theta=1; theta <=npar; theta++)
+             cptj2= (j2-1)*nlstate+i2;
-         trgradg[j][theta]=gradg[theta][j];
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-     for(i=1;i<=nlstate;i++)
+           }
-       varpl[i][(int)age] =0.;
+       }
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     fprintf(ficrescveij,"\n");
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-     for(i=1;i<=nlstate;i++)
+   }
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     fprintf(ficresvpl,"%.0f ",age );
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     for(i=1; i<=nlstate;i++)
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficresvpl,"\n");
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     free_vector(gp,1,nlstate);
+   printf("\n");
-     free_vector(gm,1,nlstate);
+   fprintf(ficlog,"\n");
-     free_matrix(gradg,1,npar,1,nlstate);
-     free_matrix(trgradg,1,nlstate,1,npar);
+   free_vector(xm,1,npar);
-   } /* End age */
+   free_vector(xp,1,npar);
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_vector(xp,1,npar);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_matrix(doldm,1,nlstate,1,npar);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+ }
- }
+ /************ Variance ******************/
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
- /************ Variance of one-step probabilities  ******************/
+ {
- 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[])
+   /* Variance of health expectancies */
- {
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   int i, j=0,  i1, k1, l1, t, tj;
+   /* double **newm;*/
-   int k2, l2, j1,  z1;
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-   int k=0,l, cptcode;
-   int first=1, first1;
+   int movingaverage();
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   double **dnewm,**doldm;
-   double **dnewm,**doldm;
+   double **dnewmp,**doldmp;
-   double *xp;
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   double *gp, *gm;
+   int k;
-   double **gradg, **trgradg;
+   double *xp;
-   double **mu;
+   double **gp, **gm;  /* for var eij */
-   double age,agelim, cov[NCOVMAX];
+   double ***gradg, ***trgradg; /*for var eij */
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   double **gradgp, **trgradgp; /* for var p point j */
-   int theta;
+   double *gpp, *gmp; /* for var p point j */
-   char fileresprob[FILENAMELENGTH];
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   char fileresprobcov[FILENAMELENGTH];
+   double ***p3mat;
-   char fileresprobcor[FILENAMELENGTH];
+   double age,agelim, hf;
+   double ***mobaverage;
-   double ***varpij;
+   int theta;
+   char digit[4];
-   strcpy(fileresprob,"prob");
+   char digitp[25];
-   strcat(fileresprob,fileres);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   char fileresprobmorprev[FILENAMELENGTH];
-     printf("Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   if(popbased==1){
-   }
+     if(mobilav!=0)
-   strcpy(fileresprobcov,"probcov");
+       strcpy(digitp,"-populbased-mobilav-");
-   strcat(fileresprobcov,fileres);
+     else strcpy(digitp,"-populbased-nomobil-");
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   }
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   else
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+     strcpy(digitp,"-stablbased-");
-   }
-   strcpy(fileresprobcor,"probcor");
+   if (mobilav!=0) {
-   strcat(fileresprobcor,fileres);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   }
+     }
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   }
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   strcpy(fileresprobmorprev,"prmorprev");
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   sprintf(digit,"%-d",ij);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   pstamp(ficresprob);
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   strcat(fileresprobmorprev,fileres);
-   fprintf(ficresprob,"# Age");
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   pstamp(ficresprobcov);
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   fprintf(ficresprobcov,"# Age");
+   }
-   pstamp(ficresprobcor);
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"# Age");
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-     for(j=1; j<=(nlstate+ndeath);j++){
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-     }
+   }
-  /* fprintf(ficresprob,"\n");
+   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficresprobcov,"\n");
+   fprintf(ficgp,"\n# Routine varevsij");
-   fprintf(ficresprobcor,"\n");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-  */
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-  xp=vector(1,npar);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ /*   } */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   pstamp(ficresvij);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   first=1;
+   if(popbased==1)
-   fprintf(ficgp,"\n# Routine varprob");
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   else
-   fprintf(fichtm,"\n");
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   fprintf(ficresvij,"# Age");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   for(i=1; i<=nlstate;i++)
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+     for(j=1; j<=nlstate;j++)
-   file %s<br>\n",optionfilehtmcov);
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   fprintf(ficresvij,"\n");
- and drawn. It helps understanding how is the covariance between two incidences.\
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   xp=vector(1,npar);
-   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. \
+   dnewm=matrix(1,nlstate,1,npar);
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   doldm=matrix(1,nlstate,1,nlstate);
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
- standard deviations wide on each axis. <br>\
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   gradgp=matrix(1,npar,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");
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-   cov[1]=1;
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   tj=cptcoveff;
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   if(estepm < stepm){
-   j1=0;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   for(t=1; t<=tj;t++){
+   }
-     for(i1=1; i1<=ncodemax[t];i1++){
+   else  hstepm=estepm;
-       j1++;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-       if  (cptcovn>0) {
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-         fprintf(ficresprob, "\n#********** Variable ");
+      nhstepm is the number of hstepm from age to agelim
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      nstepm is the number of stepm from age to agelin.
-         fprintf(ficresprob, "**********\n#\n");
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-         fprintf(ficresprobcov, "\n#********** Variable ");
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      survival function given by stepm (the optimization length). Unfortunately it
-         fprintf(ficresprobcov, "**********\n#\n");
+      means that if the survival funtion is printed every two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         fprintf(ficgp, "\n#********** Variable ");
+      results. So we changed our mind and took the option of the best precision.
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   */
-         fprintf(ficgp, "**********\n#\n");
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim = AGESUP;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+     gp=matrix(0,nhstepm,1,nlstate);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     gm=matrix(0,nhstepm,1,nlstate);
-         fprintf(ficresprobcor, "**********\n#");
-       }
+     for(theta=1; theta <=npar; theta++){
-       for (age=bage; age<=fage; age ++){
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         cov[2]=age;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         for (k=1; k<=cptcovn;k++) {
+       }
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (k=1; k<=cptcovprod;k++)
+       if (popbased==1) {
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+             prlim[i][i]=probs[(int)age][i][ij];
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         }else{ /* mobilav */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+           for(i=1; i<=nlstate;i++)
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-         for(theta=1; theta <=npar; theta++){
+       }
-           for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+       for(j=1; j<= nlstate; j++){
+         for(h=0; h<=nhstepm; h++){
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-           k=0;
+         }
-           for(i=1; i<= (nlstate); i++){
+       }
-             for(j=1; j<=(nlstate+ndeath);j++){
+       /* This for computing probability of death (h=1 means
-               k=k+1;
+          computed over hstepm matrices product = hstepm*stepm months)
-               gp[k]=pmmij[i][j];
+          as a weighted average of prlim.
-             }
+       */
-           }
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           for(i=1; i<=npar; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+       }
+       /* end probability of death */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           k=0;
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-           for(i=1; i<=(nlstate); i++){
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-             for(j=1; j<=(nlstate+ndeath);j++){
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-               k=k+1;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-               gm[k]=pmmij[i][j];
-             }
+       if (popbased==1) {
-           }
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+             prlim[i][i]=probs[(int)age][i][ij];
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         }else{ /* mobilav */
-         }
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+         }
-           for(theta=1; theta <=npar; theta++)
+       }
-             trgradg[j][theta]=gradg[theta][j];
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+         for(h=0; h<=nhstepm; h++){
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+         }
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       }
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+          as a weighted average of prlim.
+       */
-         k=0;
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1; i<=(nlstate); i++){
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-           for(j=1; j<=(nlstate+ndeath);j++){
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-             k=k+1;
+       }
-             mu[k][(int) age]=pmmij[i][j];
+       /* end probability of death */
-           }
-         }
+       for(j=1; j<= nlstate; j++) /* vareij */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+         for(h=0; h<=nhstepm; h++){
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-             varpij[i][j][(int)age] = doldm[i][j];
+         }
-         /*printf("\n%d ",(int)age);
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+       }
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
+     } /* End theta */
-         fprintf(ficresprob,"\n%d ",(int)age);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     for(h=0; h<=nhstepm; h++) /* veij */
+       for(j=1; j<=nlstate;j++)
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+         for(theta=1; theta <=npar; theta++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+           trgradg[h][j][theta]=gradg[h][theta][j];
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+       for(theta=1; theta <=npar; theta++)
-         }
+         trgradgp[j][theta]=gradgp[theta][j];
-         i=0;
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-             i=i++;
+     for(i=1;i<=nlstate;i++)
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+       for(j=1;j<=nlstate;j++)
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+         vareij[i][j][(int)age] =0.;
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+     for(h=0;h<=nhstepm;h++){
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+       for(k=0;k<=nhstepm;k++){
-             }
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-           }
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         }/* end of loop for state */
+         for(i=1;i<=nlstate;i++)
-       } /* end of loop for age */
+           for(j=1;j<=nlstate;j++)
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-       /* Confidence intervalle of pij  */
+       }
-       /*
+     }
-         fprintf(ficgp,"\nset noparametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     /* pptj */
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-         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);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+         varppt[j][i]=doldmp[j][i];
-       */
+     /* end ppptj */
+     /*  x centered again */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-       first1=1;
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+     if (popbased==1) {
-           if(l2==k2) continue;
+       if(mobilav ==0){
-           j=(k2-1)*(nlstate+ndeath)+l2;
+         for(i=1; i<=nlstate;i++)
-           for (k1=1; k1<=(nlstate);k1++){
+           prlim[i][i]=probs[(int)age][i][ij];
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+       }else{ /* mobilav */
-               if(l1==k1) continue;
+         for(i=1; i<=nlstate;i++)
-               i=(k1-1)*(nlstate+ndeath)+l1;
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-               if(i<=j) continue;
+       }
-               for (age=bage; age<=fage; age ++){
+     }
-                 if ((int)age %5==0){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+     /* This for computing probability of death (h=1 means
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+        as a weighted average of prlim.
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+     */
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                   c12=cv12/sqrt(v1*v2);
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-                   /* Computing eigen value of matrix of covariance */
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     }
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     /* end probability of death */
-                   /* Eigen vectors */
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-                   v21=(lc1-v1)/cv12*v11;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-                   v12=-v21;
+       for(i=1; i<=nlstate;i++){
-                   v22=v11;
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-                   tnalp=v21/v11;
+       }
-                   if(first1==1){
+     }
-                     first1=0;
+     fprintf(ficresprobmorprev,"\n");
-                     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(ficresvij,"%.0f ",age );
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+     for(i=1; i<=nlstate;i++)
-                   /*printf(fignu*/
+       for(j=1; j<=nlstate;j++){
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+       }
-                   if(first==1){
+     fprintf(ficresvij,"\n");
-                     first=0;
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                     fprintf(ficgp,"\nset parametric;unset label");
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                     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_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+   } /* End age */
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(gradgp,1,npar,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_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-                     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 replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                   }else{
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                     first=0;
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   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,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+ */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                   }/* if first */
-                 } /* age mod 5 */
+   free_vector(xp,1,npar);
-               } /* end loop age */
+   free_matrix(doldm,1,nlstate,1,nlstate);
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(dnewm,1,nlstate,1,npar);
-               first=1;
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-             } /*l12 */
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-           } /* k12 */
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         } /*l1 */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       }/* k1 */
+   fclose(ficresprobmorprev);
-     } /* loop covariates */
+   fflush(ficgp);
-   }
+   fflush(fichtm);
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+ }  /* end varevsij */
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ /************ Variance of prevlim ******************/
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
-   free_vector(xp,1,npar);
+ {
-   fclose(ficresprob);
+   /* Variance of prevalence limit */
-   fclose(ficresprobcov);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   fclose(ficresprobcor);
-   fflush(ficgp);
+   double **dnewm,**doldm;
-   fflush(fichtmcov);
+   int i, j, nhstepm, hstepm;
- }
+   double *xp;
+   double *gp, *gm;
+   double **gradg, **trgradg;
- /******************* Printing html file ***********/
+   double age,agelim;
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   int theta;
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   pstamp(ficresvpl);
-                   int popforecast, int estepm ,\
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-                   double jprev1, double mprev1,double anprev1, \
+   fprintf(ficresvpl,"# Age");
-                   double jprev2, double mprev2,double anprev2){
+   for(i=1; i<=nlstate;i++)
-   int jj1, k1, i1, cpt;
+       fprintf(ficresvpl," %1d-%1d",i,i);
+   fprintf(ficresvpl,"\n");
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   xp=vector(1,npar);
- </ul>");
+   dnewm=matrix(1,nlstate,1,npar);
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   doldm=matrix(1,nlstate,1,nlstate);
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   hstepm=1*YEARM; /* Every year of age */
-    fprintf(fichtm,"\
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   agelim = AGESUP;
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-    fprintf(fichtm,"\
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+     if (stepm >= YEARM) hstepm=1;
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-    fprintf(fichtm,"\
+     gradg=matrix(1,npar,1,nlstate);
-  - (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): \
+     gp=vector(1,nlstate);
-    <a href=\"%s\">%s</a> <br>\n",
+     gm=vector(1,nlstate);
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-    fprintf(fichtm,"\
+     for(theta=1; theta <=npar; theta++){
-  - Population projections by age and states: \
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       for(i=1;i<=nlstate;i++)
-  m=cptcoveff;
+         gp[i] = prlim[i][i];
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       for(i=1; i<=npar; i++) /* Computes gradient */
-  jj1=0;
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-  for(k1=1; k1<=m;k1++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+       for(i=1;i<=nlstate;i++)
-      jj1++;
+         gm[i] = prlim[i][i];
-      if (cptcovn > 0) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+       for(i=1;i<=nlstate;i++)
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     } /* End theta */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-      }
+     trgradg =matrix(1,nlstate,1,npar);
-      /* 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> \
+     for(j=1; j<=nlstate;j++)
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       for(theta=1; theta <=npar; theta++)
-      /* Quasi-incidences */
+         trgradg[j][theta]=gradg[theta][j];
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+     for(i=1;i<=nlstate;i++)
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       varpl[i][(int)age] =0.;
-        /* Period (stable) prevalence in each health state */
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-        for(cpt=1; cpt<nlstate;cpt++){
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+     for(i=1;i<=nlstate;i++)
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-        }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+     fprintf(ficresvpl,"%.0f ",age );
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+     for(i=1; i<=nlstate;i++)
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-      }
+     fprintf(ficresvpl,"\n");
-    } /* end i1 */
+     free_vector(gp,1,nlstate);
-  }/* End k1 */
+     free_vector(gm,1,nlstate);
-  fprintf(fichtm,"</ul>");
+     free_matrix(gradg,1,npar,1,nlstate);
+     free_matrix(trgradg,1,nlstate,1,npar);
+   } /* End age */
-  fprintf(fichtm,"\
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   free_vector(xp,1,npar);
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+ }
-  fprintf(fichtm,"\
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ /************ Variance of one-step probabilities  ******************/
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+ {
-  fprintf(fichtm,"\
+   int i, j=0,  k1, l1, tj;
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   int k2, l2, j1,  z1;
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   int k=0, l;
-  fprintf(fichtm,"\
+   int first=1, first1, first2;
-  - 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): \
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   double **dnewm,**doldm;
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   double *xp;
-  fprintf(fichtm,"\
+   double *gp, *gm;
-  - (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 **gradg, **trgradg;
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   double **mu;
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   double age, cov[NCOVMAX+1];
-  fprintf(fichtm,"\
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-  - 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",
+   int theta;
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+   char fileresprob[FILENAMELENGTH];
-  fprintf(fichtm,"\
+   char fileresprobcov[FILENAMELENGTH];
-  - 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 fileresprobcor[FILENAMELENGTH];
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   double ***varpij;
-  fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   strcpy(fileresprob,"prob");
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   strcat(fileresprob,fileres);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+     printf("Problem with resultfile: %s\n", fileresprob);
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   }
- /*      <br>",fileres,fileres,fileres,fileres); */
+   strcpy(fileresprobcov,"probcov");
- /*  else  */
+   strcat(fileresprobcov,fileres);
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-  fflush(fichtm);
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
-  m=cptcoveff;
+   strcpy(fileresprobcor,"probcor");
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-  jj1=0;
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-  for(k1=1; k1<=m;k1++){
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   }
-      jj1++;
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-      if (cptcovn > 0) {
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-      }
+   pstamp(ficresprob);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   fprintf(ficresprob,"# Age");
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   pstamp(ficresprobcov);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-      }
+   fprintf(ficresprobcov,"# Age");
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   pstamp(ficresprobcor);
- health expectancies in states (1) and (2): %s%d.png<br>\
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+   fprintf(ficresprobcor,"# Age");
-    } /* end i1 */
-  }/* End k1 */
-  fprintf(fichtm,"</ul>");
+   for(i=1; i<=nlstate;i++)
-  fflush(fichtm);
+     for(j=1; j<=(nlstate+ndeath);j++){
- }
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
- /******************* Gnuplot file **************/
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     }
+  /* fprintf(ficresprob,"\n");
-   char dirfileres[132],optfileres[132];
+   fprintf(ficresprobcov,"\n");
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   fprintf(ficresprobcor,"\n");
-   int ng;
+  */
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+   xp=vector(1,npar);
- /*     printf("Problem with file %s",optionfilegnuplot); */
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- /*   } */
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   /*#ifdef windows */
+   first=1;
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   fprintf(ficgp,"\n# Routine varprob");
-     /*#endif */
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   m=pow(2,cptcoveff);
+   fprintf(fichtm,"\n");
-   strcpy(dirfileres,optionfilefiname);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   strcpy(optfileres,"vpl");
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-  /* 1eme*/
+   file %s<br>\n",optionfilehtmcov);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-    for (k1=1; k1<= m ; k1 ++) {
+ and drawn. It helps understanding how is the covariance between two incidences.\
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
- set ylabel \"Probability\" \n\
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
- set ter png small\n\
+ standard deviations wide on each axis. <br>\
- set size 0.65,0.65\n\
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-      for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   cov[1]=1;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   /* tj=cptcoveff; */
-      }
+   tj = (int) pow(2,cptcoveff);
-      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);
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-      for (i=1; i<= nlstate ; i ++) {
+   j1=0;
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   for(j1=1; j1<=tj;j1++){
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-      }
+     /*j1++;*/
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+       if  (cptcovn>0) {
-      for (i=1; i<= nlstate ; i ++) {
+         fprintf(ficresprob, "\n#********** Variable ");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprob, "**********\n#\n");
-      }
+         fprintf(ficresprobcov, "\n#********** Variable ");
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    }
+         fprintf(ficresprobcov, "**********\n#\n");
-   }
-   /*2 eme*/
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (k1=1; k1<= m ; k1 ++) {
+         fprintf(ficgp, "**********\n#\n");
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-     for (i=1; i<= nlstate+1 ; i ++) {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       k=2*i;
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+         fprintf(ficresprobcor, "\n#********** Variable ");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprobcor, "**********\n#");
        }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       for (j=1; j<= nlstate+1 ; j ++) {
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       for (age=bage; age<=fage; age ++){
-       }
+         cov[2]=age;
-       fprintf(ficgp,"\" t\"\" w l 0,");
+         for (k=1; k<=cptcovn;k++) {
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                          * 1  1 1 1 1
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                                                          * 2  2 1 1 1
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                                          * 3  1 2 1 1
-       }
+                                                          */
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+         }
-     }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-   }
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
+         for(theta=1; theta <=npar; theta++){
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+           for(i=1; i<=npar; i++)
-       /*       k=2+nlstate*(2*cpt-2); */
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       fprintf(ficgp,"set ter png small\n\
- set size 0.65,0.65\n\
+           k=0;
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+           for(i=1; i<= (nlstate); i++){
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+             for(j=1; j<=(nlstate+ndeath);j++){
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+               k=k+1;
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+               gp[k]=pmmij[i][j];
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+             }
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           }
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           for(i=1; i<=npar; i++)
-       */
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-       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);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-         /*      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);*/
+           k=0;
+           for(i=1; i<=(nlstate); i++){
-       }
+             for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+               k=k+1;
-     }
+               gm[k]=pmmij[i][j];
-   }
+             }
+           }
-   /* CV preval stable (period) */
-   for (k1=1; k1<= m ; k1 ++) {
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-       k=3;
+         }
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
- set ter png small\nset size 0.65,0.65\n\
+           for(theta=1; theta <=npar; theta++)
- unset log y\n\
+             trgradg[j][theta]=gradg[theta][j];
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       for (i=1; i< nlstate ; i ++)
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         fprintf(ficgp,"+$%d",k+i+1);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-       l=3+(nlstate+ndeath)*cpt;
+         k=0;
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+         for(i=1; i<=(nlstate); i++){
-       for (i=1; i< nlstate ; i ++) {
+           for(j=1; j<=(nlstate+ndeath);j++){
-         l=3+(nlstate+ndeath)*cpt;
+             k=k+1;
-         fprintf(ficgp,"+$%d",l+i+1);
+             mu[k][(int) age]=pmmij[i][j];
-       }
+           }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+         }
-     }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-   }
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             varpij[i][j][(int)age] = doldm[i][j];
-   /* proba elementaires */
-   for(i=1,jk=1; i <=nlstate; i++){
+         /*printf("\n%d ",(int)age);
-     for(k=1; k <=(nlstate+ndeath); k++){
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       if (k != i) {
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           }*/
-           jk++;
-           fprintf(ficgp,"\n");
+         fprintf(ficresprob,"\n%d ",(int)age);
-         }
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-       }
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-     }
-    }
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-    for(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(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-        if (ng==2)
+         }
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+         i=0;
-        else
+         for (k=1; k<=(nlstate);k++){
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+           for (l=1; l<=(nlstate+ndeath);l++){
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+             i++;
-        i=1;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-        for(k2=1; k2<=nlstate; k2++) {
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-          k3=i;
+             for (j=1; j<=i;j++){
-          for(k=1; k<=(nlstate+ndeath); k++) {
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-            if (k != k2){
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-              if(ng==2)
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+             }
-              else
+           }
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+         }/* end of loop for state */
-              ij=1;
+       } /* end of loop for age */
-              for(j=3; j <=ncovmodel; j++) {
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                  ij++;
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                }
-                else
+       /* Confidence intervalle of pij  */
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       /*
-              }
+         fprintf(ficgp,"\nunset parametric;unset label");
-              fprintf(ficgp,")/(1");
+         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");
-              for(k1=1; k1 <=nlstate; k1++){
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-                ij=1;
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-                for(j=3; j <=ncovmodel; j++){
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       */
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-                    ij++;
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-                  }
+       first1=1;first2=2;
-                  else
+       for (k2=1; k2<=(nlstate);k2++){
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-                }
+           if(l2==k2) continue;
-                fprintf(ficgp,")");
+           j=(k2-1)*(nlstate+ndeath)+l2;
-              }
+           for (k1=1; k1<=(nlstate);k1++){
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+               if(l1==k1) continue;
-              i=i+ncovmodel;
+               i=(k1-1)*(nlstate+ndeath)+l1;
-            }
+               if(i<=j) continue;
-          } /* end k */
+               for (age=bage; age<=fage; age ++){
-        } /* end k2 */
+                 if ((int)age %5==0){
-      } /* end jk */
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-    } /* end ng */
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-    fflush(ficgp);
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
- }  /* end gnuplot */
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
+                   c12=cv12/sqrt(v1*v2);
- /*************** Moving average **************/
+                   /* Computing eigen value of matrix of covariance */
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   int i, cpt, cptcod;
+                   if ((lc2 <0) || (lc1 <0) ){
-   int modcovmax =1;
+                     if(first2==1){
-   int mobilavrange, mob;
+                       first1=0;
-   double age;
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     }
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                     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);
-                            a covariate has 2 modalities */
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                     /* lc2=fabs(lc2); */
+                   }
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-     if(mobilav==1) mobilavrange=5; /* default */
+                   /* Eigen vectors */
-     else mobilavrange=mobilav;
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-     for (age=bage; age<=fage; age++)
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-       for (i=1; i<=nlstate;i++)
+                   v21=(lc1-v1)/cv12*v11;
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                   v12=-v21;
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                   v22=v11;
-     /* We keep the original values on the extreme ages bage, fage and for
+                   tnalp=v21/v11;
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                   if(first1==1){
-        we use a 5 terms etc. until the borders are no more concerned.
+                     first1=0;
-     */
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                   }
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-         for (i=1; i<=nlstate;i++){
+                   /*printf(fignu*/
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                   if(first==1){
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                     first=0;
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                     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);
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-           }
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-         }
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-       }/* end age */
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-     }/* end mob */
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-   }else return -1;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   return 0;
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- }/* End movingaverage */
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- /************** Forecasting ******************/
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, 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,"\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",\
-   /* proj1, year, month, day of starting projection
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-      agemin, agemax range of age
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+                   }else{
-      anproj2 year of en of projection (same day and month as proj1).
+                     first=0;
-   */
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   int *popage;
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   double agec; /* generic age */
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   double *popeffectif,*popcount;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   double ***p3mat;
+                   }/* if first */
-   double ***mobaverage;
+                 } /* age mod 5 */
-   char fileresf[FILENAMELENGTH];
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   agelim=AGESUP;
+               first=1;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+             } /*l12 */
+           } /* k12 */
-   strcpy(fileresf,"f");
+         } /*l1 */
-   strcat(fileresf,fileres);
+       }/* k1 */
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+       /* } */ /* loop covariates */
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+   }
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   }
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   free_vector(xp,1,npar);
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   fclose(ficresprob);
+   fclose(ficresprobcov);
-   if (mobilav!=0) {
+   fclose(ficresprobcor);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fflush(ficgp);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   fflush(fichtmcov);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ }
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+                   int lastpass, int stepm, int weightopt, char model[],\
-   if (stepm<=12) stepsize=1;
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   if(estepm < stepm){
+                   int popforecast, int estepm ,\
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+                   double jprev1, double mprev1,double anprev1, \
-   }
+                   double jprev2, double mprev2,double anprev2){
-   else  hstepm=estepm;
+   int jj1, k1, i1, cpt;
-   hstepm=hstepm/stepm;
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-                                fractional in yp1 */
+ </ul>");
-   anprojmean=yp;
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-   yp2=modf((yp1*12),&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 ",
-   mprojmean=yp;
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   yp1=modf((yp2*30.5),&yp);
+    fprintf(fichtm,"\
-   jprojmean=yp;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-   if(jprojmean==0) jprojmean=1;
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   if(mprojmean==0) jprojmean=1;
+    fprintf(fichtm,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-   i1=cptcoveff;
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-   if (cptcovn < 1){i1=1;}
+    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,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
- /*            if (h==(int)(YEARM*yearp)){ */
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-       k=k+1;
-       fprintf(ficresf,"\n#******");
+  m=pow(2,cptcoveff);
-       for(j=1;j<=cptcoveff;j++) {
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-         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]]);
-       }
+  jj1=0;
-       fprintf(ficresf,"******\n");
+  for(k1=1; k1<=m;k1++){
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+    for(i1=1; i1<=ncodemax[k1];i1++){
-       for(j=1; j<=nlstate+ndeath;j++){
+      jj1++;
-         for(i=1; i<=nlstate;i++)
+      if (cptcovn > 0) {
-           fprintf(ficresf," p%d%d",i,j);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-         fprintf(ficresf," p.%d",j);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-       }
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-         fprintf(ficresf,"\n");
+      }
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+      /* 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%d_1.png\">%s%d_1.png</a><br> \
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+      /* Quasi-incidences */
-           nhstepm = nhstepm/hstepm;
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  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> \
-           oldm=oldms;savm=savms;
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+        /* Period (stable) prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
-           for (h=0; h<=nhstepm; h++){
+          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> \
-             if (h*hstepm/YEARM*stepm ==yearp) {
+ <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,"\n");
+        }
-               for(j=1;j<=cptcoveff;j++)
+      for(cpt=1; cpt<=nlstate;cpt++) {
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         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> \
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-             }
+      }
-             for(j=1; j<=nlstate+ndeath;j++) {
+    } /* end i1 */
-               ppij=0.;
+  }/* End k1 */
-               for(i=1; i<=nlstate;i++) {
+  fprintf(fichtm,"</ul>");
-                 if (mobilav==1)
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-                 else {
+  fprintf(fichtm,"\
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-                 }
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-                 if (h*hstepm/YEARM*stepm== yearp) {
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                 }
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-               } /* end i */
+  fprintf(fichtm,"\
-               if (h*hstepm/YEARM*stepm==yearp) {
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                 fprintf(ficresf," %.3f", ppij);
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-               }
-             }/* end j */
+  fprintf(fichtm,"\
-           } /* end h */
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-         } /* end agec */
+  fprintf(fichtm,"\
-       } /* end yearp */
+  - 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): \
-     } /* end cptcod */
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   } /* end  cptcov */
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  - (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>",
-   fclose(ficresf);
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
- }
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
- /************** Forecasting *****not tested NB*************/
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+  fprintf(fichtm,"\
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   int *popage;
+  fprintf(fichtm,"\
-   double calagedatem, agelim, kk1, kk2;
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-   double *popeffectif,*popcount;
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   char filerespop[FILENAMELENGTH];
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*      <br>",fileres,fileres,fileres,fileres); */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*  else  */
-   agelim=AGESUP;
+ /*    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); */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  m=pow(2,cptcoveff);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   strcpy(filerespop,"pop");
-   strcat(filerespop,fileres);
+  jj1=0;
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+  for(k1=1; k1<=m;k1++){
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+    for(i1=1; i1<=ncodemax[k1];i1++){
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+      jj1++;
-   }
+      if (cptcovn > 0) {
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
-   if (mobilav!=0) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+      }
-     }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   }
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+  drawn in addition to the population based expectancies computed using\
-   if (stepm<=12) stepsize=1;
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   agelim=AGESUP;
+    } /* end i1 */
+  }/* End k1 */
-   hstepm=1;
+  fprintf(fichtm,"</ul>");
-   hstepm=hstepm/stepm;
+  fflush(fichtm);
+ }
-   if (popforecast==1) {
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /******************* Gnuplot file **************/
-       printf("Problem with population file : %s\n",popfile);exit(0);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-     }
+   char dirfileres[132],optfileres[132];
-     popage=ivector(0,AGESUP);
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-     popeffectif=vector(0,AGESUP);
+   int ng=0;
-     popcount=vector(0,AGESUP);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     i=1;
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*   } */
-     imx=i;
+   /*#ifdef windows */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   }
+     /*#endif */
+   m=pow(2,cptcoveff);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   strcpy(dirfileres,optionfilefiname);
-       k=k+1;
+   strcpy(optfileres,"vpl");
-       fprintf(ficrespop,"\n#******");
+  /* 1eme*/
-       for(j=1;j<=cptcoveff;j++) {
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-       }
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       fprintf(ficrespop,"******\n");
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-       fprintf(ficrespop,"# Age");
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ set ylabel \"Probability\" \n\
+ set ter png small size 320, 240\n\
-       for (cpt=0; cpt<=0;cpt++) {
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+      for (i=1; i<= nlstate ; i ++) {
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-           nhstepm = nhstepm/hstepm;
+      }
+      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);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      for (i=1; i<= nlstate ; i ++) {
-           oldm=oldms;savm=savms;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+        else fprintf(ficgp," %%*lf (%%*lf)");
+      }
-           for (h=0; h<=nhstepm; h++){
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+      for (i=1; i<= nlstate ; i ++) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-             }
+        else fprintf(ficgp," %%*lf (%%*lf)");
-             for(j=1; j<=nlstate+ndeath;j++) {
+      }
-               kk1=0.;kk2=0;
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-               for(i=1; i<=nlstate;i++) {
+    }
-                 if (mobilav==1)
+   }
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+   /*2 eme*/
-                 else {
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+   for (k1=1; k1<= m ; k1 ++) {
-                 }
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-               }
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-               if (h==(int)(calagedatem+12*cpt)){
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+     for (i=1; i<= nlstate+1 ; i ++) {
-                   /*fprintf(ficrespop," %.3f", kk1);
+       k=2*i;
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-               }
+       for (j=1; j<= nlstate+1 ; j ++) {
-             }
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-             for(i=1; i<=nlstate;i++){
+         else fprintf(ficgp," %%*lf (%%*lf)");
-               kk1=0.;
+       }
-                 for(j=1; j<=nlstate;j++){
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+       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);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+       for (j=1; j<= nlstate+1 ; j ++) {
-             }
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
+         else fprintf(ficgp," %%*lf (%%*lf)");
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+       }
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-           }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (j=1; j<= nlstate+1 ; j ++) {
-         }
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       }
+         else fprintf(ficgp," %%*lf (%%*lf)");
+       }
-   /******/
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+     }
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   }
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   /*3eme*/
-           nhstepm = nhstepm/hstepm;
+   for (k1=1; k1<= m ; k1 ++) {
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-           oldm=oldms;savm=savms;
+       /*       k=2+nlstate*(2*cpt-2); */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       k=2+(nlstate+1)*(cpt-1);
-           for (h=0; h<=nhstepm; h++){
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-             }
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-             for(j=1; j<=nlstate+ndeath;j++) {
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-               kk1=0.;kk2=0;
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-               for(i=1; i<=nlstate;i++) {
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-               }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-             }
+       */
-           }
+       for (i=1; i< nlstate ; i ++) {
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         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);*/
-       }
-    }
+       }
-   }
+       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 (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }
-   if (popforecast==1) {
+   /* CV preval stable (period) */
-     free_ivector(popage,0,AGESUP);
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-     free_vector(popeffectif,0,AGESUP);
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-     free_vector(popcount,0,AGESUP);
+       k=3;
-   }
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-   fclose(ficrespop);
+ set ter png small size 320, 240\n\
- } /* End of popforecast */
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
- int fileappend(FILE *fichier, char *optionfich)
+       for (i=1; i<= nlstate ; i ++){
- {
+         if(i==1)
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-     printf("Problem with file: %s\n", optionfich);
+         else
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+           fprintf(ficgp,", '' ");
-     return (0);
+         l=(nlstate+ndeath)*(i-1)+1;
-   }
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   fflush(fichier);
+         for (j=1; j<= (nlstate-1) ; j ++)
-   return (1);
+           fprintf(ficgp,"+$%d",k+l+j);
- }
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\n");
- /**************** function prwizard **********************/
+     } /* end cpt state*/
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+   } /* end covariate */
- {
+   /* proba elementaires */
-   /* Wizard to print covariance matrix template */
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
-   char ca[32], cb[32], cc[32];
+       if (k != i) {
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+         for(j=1; j <=ncovmodel; j++){
-   int numlinepar;
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           fprintf(ficgp,"\n");
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         }
-   for(i=1; i <=nlstate; i++){
+       }
-     jj=0;
+     }
-     for(j=1; j <=nlstate+ndeath; j++){
+    }
-       if(j==i) continue;
+   /*goto avoid;*/
-       jj++;
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+      for(jk=1; jk <=m; jk++) {
-       printf("%1d%1d",i,j);
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-       fprintf(ficparo,"%1d%1d",i,j);
+        if (ng==2)
-       for(k=1; k<=ncovmodel;k++){
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-         /*        printf(" %lf",param[i][j][k]); */
+        else
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-         printf(" 0.");
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-         fprintf(ficparo," 0.");
+        i=1;
-       }
+        for(k2=1; k2<=nlstate; k2++) {
-       printf("\n");
+          k3=i;
-       fprintf(ficparo,"\n");
+          for(k=1; k<=(nlstate+ndeath); k++) {
-     }
+            if (k != k2){
-   }
+              if(ng==2)
-   printf("# Scales (for hessian or gradient estimation)\n");
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+              else
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-   for(i=1; i <=nlstate; i++){
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-     jj=0;
+              for(j=3; j <=ncovmodel; j++) {
-     for(j=1; j <=nlstate+ndeath; j++){
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-       if(j==i) continue;
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-       jj++;
+                /*        ij++; */
-       fprintf(ficparo,"%1d%1d",i,j);
+                /* } */
-       printf("%1d%1d",i,j);
+                /* else */
-       fflush(stdout);
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       for(k=1; k<=ncovmodel;k++){
+              }
-         /*      printf(" %le",delti3[i][j][k]); */
+              fprintf(ficgp,")/(1");
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-         printf(" 0.");
+              for(k1=1; k1 <=nlstate; k1++){
-         fprintf(ficparo," 0.");
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-       }
+                ij=1;
-       numlinepar++;
+                for(j=3; j <=ncovmodel; j++){
-       printf("\n");
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-       fprintf(ficparo,"\n");
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-     }
+                  /*   ij++; */
-   }
+                  /* } */
-   printf("# Covariance matrix\n");
+                  /* else */
- /* # 121 Var(a12)\n\ */
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                }
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                fprintf(ficgp,")");
- /* # 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,") t \"p%d%d\" ", k2,k);
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+              i=i+ncovmodel;
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+            }
-   fflush(stdout);
+          } /* end k */
-   fprintf(ficparo,"# Covariance matrix\n");
+        } /* end k2 */
-   /* # 121 Var(a12)\n\ */
+      } /* end jk */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+    } /* end ng */
-   /* #   ...\n\ */
+  /* avoid: */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+    fflush(ficgp);
+ }  /* end gnuplot */
-   for(itimes=1;itimes<=2;itimes++){
-     jj=0;
-     for(i=1; i <=nlstate; i++){
+ /*************** Moving average **************/
-       for(j=1; j <=nlstate+ndeath; j++){
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-         if(j==i) continue;
-         for(k=1; k<=ncovmodel;k++){
+   int i, cpt, cptcod;
-           jj++;
+   int modcovmax =1;
-           ca[0]= k+'a'-1;ca[1]='\0';
+   int mobilavrange, mob;
-           if(itimes==1){
+   double age;
-             printf("#%1d%1d%d",i,j,k);
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-           }else{
+                            a covariate has 2 modalities */
-             printf("%1d%1d%d",i,j,k);
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
-             /*  printf(" %.5le",matcov[i][j]); */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-           }
+     if(mobilav==1) mobilavrange=5; /* default */
-           ll=0;
+     else mobilavrange=mobilav;
-           for(li=1;li <=nlstate; li++){
+     for (age=bage; age<=fage; age++)
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+       for (i=1; i<=nlstate;i++)
-               if(lj==li) continue;
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-               for(lk=1;lk<=ncovmodel;lk++){
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-                 ll++;
+     /* 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
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+        we use a 5 terms etc. until the borders are no more concerned.
-                   if(ll<jj){
+     */
-                     if(itimes==1){
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         for (i=1; i<=nlstate;i++){
-                     }else{
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-                       printf(" 0.");
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-                       fprintf(ficparo," 0.");
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-                     }
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                   }else{
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-                     if(itimes==1){
+               }
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+           }
-                     }else{
+         }
-                       printf(" 0.");
+       }/* end age */
-                       fprintf(ficparo," 0.");
+     }/* end mob */
-                     }
+   }else return -1;
-                   }
+   return 0;
-                 }
+ }/* End movingaverage */
-               } /* end lk */
-             } /* end lj */
-           } /* end li */
+ /************** Forecasting ******************/
-           printf("\n");
+ 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){
-           fprintf(ficparo,"\n");
+   /* proj1, year, month, day of starting projection
-           numlinepar++;
+      agemin, agemax range of age
-         } /* end k*/
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-       } /*end j */
+      anproj2 year of en of projection (same day and month as proj1).
-     } /* end i */
+   */
-   } /* end itimes */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+   double agec; /* generic age */
- } /* end of prwizard */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- /******************* Gompertz Likelihood ******************************/
+   double *popeffectif,*popcount;
- double gompertz(double x[])
+   double ***p3mat;
- {
+   double ***mobaverage;
-   double A,B,L=0.0,sump=0.,num=0.;
+   char fileresf[FILENAMELENGTH];
-   int i,n=0; /* n is the size of the sample */
+   agelim=AGESUP;
-   for (i=0;i<=imx-1 ; i++) {
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     sump=sump+weight[i];
-     /*    sump=sump+1;*/
+   strcpy(fileresf,"f");
-     num=num+1;
+   strcat(fileresf,fileres);
-   }
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   /* 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]);*/
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   for (i=1;i<=imx ; i++)
-     {
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-       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 (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (cens[i] == 0 && wav[i]>1)
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   }
-       if (wav[i] > 1 ) { /* ??? */
-         L=L+A*weight[i];
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-         /*      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 (stepm<=12) stepsize=1;
-       }
+   if(estepm < stepm){
-     }
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   else  hstepm=estepm;
-   return -2*L*num/sump;
+   hstepm=hstepm/stepm;
- }
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
- /******************* Printing html file ***********/
+   anprojmean=yp;
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+   yp2=modf((yp1*12),&yp);
-                   int lastpass, int stepm, int weightopt, char model[],\
+   mprojmean=yp;
-                   int imx,  double p[],double **matcov,double agemortsup){
+   yp1=modf((yp2*30.5),&yp);
-   int i,k;
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+   if(mprojmean==0) jprojmean=1;
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   for (i=1;i<=2;i++)
+   i1=cptcoveff;
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   if (cptcovn < 1){i1=1;}
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   fprintf(fichtm,"</ul>");
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-  for (k=agegomp;k<(agemortsup-2);k++)
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-    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]);
+       k=k+1;
+       fprintf(ficresf,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
-   fflush(fichtm);
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
+       }
+       fprintf(ficresf,"******\n");
- /******************* Gnuplot file **************/
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
-   char dirfileres[132],optfileres[132];
+           fprintf(ficresf," p%d%d",i,j);
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+         fprintf(ficresf," p.%d",j);
-   int ng;
+       }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+         fprintf(ficresf,"\n");
-   /*#ifdef windows */
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+         for (agec=fage; agec>=(ageminpar-1); agec--){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   strcpy(dirfileres,optionfilefiname);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   strcpy(optfileres,"vpl");
+           oldm=oldms;savm=savms;
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   fprintf(ficgp, "set ter png small\n set log y\n");
+           for (h=0; h<=nhstepm; h++){
-   fprintf(ficgp, "set size 0.65,0.65\n");
+             if (h*hstepm/YEARM*stepm ==yearp) {
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+               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.;
+               for(i=1; i<=nlstate;i++) {
- /***********************************************/
+                 if (mobilav==1)
- /**************** Main Program *****************/
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
- /***********************************************/
+                 else {
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
- int main(int argc, char *argv[])
+                 }
- {
+                 if (h*hstepm/YEARM*stepm== yearp) {
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+                 }
-   int linei, month, year,iout;
+               } /* end i */
-   int jj, ll, li, lj, lk, imk;
+               if (h*hstepm/YEARM*stepm==yearp) {
-   int numlinepar=0; /* Current linenumber of parameter file */
+                 fprintf(ficresf," %.3f", ppij);
-   int itimes;
+               }
-   int NDIM=2;
+             }/* end j */
+           } /* end h */
-   char ca[32], cb[32], cc[32];
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   char dummy[]="                         ";
+         } /* end agec */
-   /*  FILE *fichtm; *//* Html File */
+       } /* end yearp */
-   /* FILE *ficgp;*/ /*Gnuplot File */
+     } /* end cptcod */
-   struct stat info;
+   } /* end  cptcov */
-   double agedeb, agefin,hf;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double fret;
+   fclose(ficresf);
-   double **xi,tmp,delta;
+ }
-   double dum; /* Dummy variable */
+ /************** Forecasting *****not tested NB*************/
-   double ***p3mat;
+ 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){
-   double ***mobaverage;
-   int *indx;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   char line[MAXLINE], linepar[MAXLINE];
+   int *popage;
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   double calagedatem, agelim, kk1, kk2;
-   char pathr[MAXLINE], pathimach[MAXLINE];
+   double *popeffectif,*popcount;
-   char **bp, *tok, *val; /* pathtot */
+   double ***p3mat,***tabpop,***tabpopprev;
-   int firstobs=1, lastobs=10;
+   double ***mobaverage;
-   int sdeb, sfin; /* Status at beginning and end */
+   char filerespop[FILENAMELENGTH];
-   int c,  h , cpt,l;
-   int ju,jl, mi;
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   agelim=AGESUP;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   int agemortsup;
-   float  sumlpop=0.;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   strcpy(filerespop,"pop");
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   double bage, fage, age, agelim, agebase;
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   double ftolpl=FTOL;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   double **prlim;
+   }
-   double *severity;
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   double ***param; /* Matrix of parameters */
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   double  *p;
-   double **matcov; /* Matrix of covariance */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
+   if (mobilav!=0) {
-   double ***eij, ***vareij;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double **varpl; /* Variances of prevalence limits by age */
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   double *epj, vepp;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   double kk1, kk2;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+     }
-   double **ximort;
+   }
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
-   int *dcwave;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   char z[1]="c", occ;
+   agelim=AGESUP;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
+   hstepm=1;
-   char *stratrunc;
+   hstepm=hstepm/stepm;
-   int lstra;
+   if (popforecast==1) {
-   long total_usecs;
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
- /*   setlocale (LC_ALL, ""); */
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+     }
- /*   textdomain (PACKAGE); */
+     popage=ivector(0,AGESUP);
- /*   setlocale (LC_CTYPE, ""); */
+     popeffectif=vector(0,AGESUP);
- /*   setlocale (LC_MESSAGES, ""); */
+     popcount=vector(0,AGESUP);
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+     i=1;
-   (void) gettimeofday(&start_time,&tzp);
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   curr_time=start_time;
-   tm = *localtime(&start_time.tv_sec);
+     imx=i;
-   tmg = *gmtime(&start_time.tv_sec);
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   strcpy(strstart,asctime(&tm));
+   }
- /*  printf("Localtime (at start)=%s",strstart); */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
- /*  tp.tv_sec = tp.tv_sec +86400; */
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- /*  tm = *localtime(&start_time.tv_sec); */
+       k=k+1;
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       fprintf(ficrespop,"\n#******");
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       for(j=1;j<=cptcoveff;j++) {
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- /*   tp.tv_sec = mktime(&tmg); */
+       }
- /*   strt=asctime(&tmg); */
+       fprintf(ficrespop,"******\n");
- /*   printf("Time(after) =%s",strstart);  */
+       fprintf(ficrespop,"# Age");
- /*  (void) time (&time_value);
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
- *  tm = *localtime(&time_value);
- *  strstart=asctime(&tm);
+       for (cpt=0; cpt<=0;cpt++) {
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   nberr=0; /* Number of errors and warnings */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   nbwarn=0;
+           nhstepm = nhstepm/hstepm;
-   getcwd(pathcd, size);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   printf("\n%s\n%s",version,fullversion);
+           oldm=oldms;savm=savms;
-   if(argc <=1){
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+           for (h=0; h<=nhstepm; h++){
-     i=strlen(pathr);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-     if(pathr[i-1]=='\n')
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       pathr[i-1]='\0';
+             }
-    for (tok = pathr; tok != NULL; ){
+             for(j=1; j<=nlstate+ndeath;j++) {
-       printf("Pathr |%s|\n",pathr);
+               kk1=0.;kk2=0;
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+               for(i=1; i<=nlstate;i++) {
-       printf("val= |%s| pathr=%s\n",val,pathr);
+                 if (mobilav==1)
-       strcpy (pathtot, val);
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-       if(pathr[0] == '\0') break; /* Dirty */
+                 else {
-     }
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-   }
+                 }
-   else{
+               }
-     strcpy(pathtot,argv[1]);
+               if (h==(int)(calagedatem+12*cpt)){
-   }
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+                   /*fprintf(ficrespop," %.3f", kk1);
-   /*cygwin_split_path(pathtot,path,optionfile);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+               }
-   /* cutv(path,optionfile,pathtot,'\\');*/
+             }
+             for(i=1; i<=nlstate;i++){
-   /* Split argv[0], imach program to get pathimach */
+               kk1=0.;
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+                 for(j=1; j<=nlstate;j++){
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+                 }
-  /*   strcpy(pathimach,argv[0]); */
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+             }
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   chdir(path); /* Can be a relative path */
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+           }
-     printf("Current directory %s!\n",pathcd);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   strcpy(command,"mkdir ");
+         }
-   strcat(command,optionfilefiname);
+       }
-   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); */
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
- /*     exit(1); */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   }
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- /*     perror("mkdir"); */
+           nhstepm = nhstepm/hstepm;
- /*   } */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /*-------- arguments in the command line --------*/
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   /* Log file */
+           for (h=0; h<=nhstepm; h++){
-   strcat(filelog, optionfilefiname);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   strcat(filelog,".log");    /* */
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+             }
-     printf("Problem with logfile %s\n",filelog);
+             for(j=1; j<=nlstate+ndeath;j++) {
-     goto end;
+               kk1=0.;kk2=0;
-   }
+               for(i=1; i<=nlstate;i++) {
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+               }
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+             }
-  path=%s \n\
+           }
-  optionfile=%s\n\
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  optionfilext=%s\n\
+         }
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+       }
+    }
-   printf("Local time (at start):%s",strstart);
+   }
-   fprintf(ficlog,"Local time (at start): %s",strstart);
-   fflush(ficlog);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
-   /* */
+     free_vector(popeffectif,0,AGESUP);
-   strcpy(fileres,"r");
+     free_vector(popcount,0,AGESUP);
-   strcat(fileres, optionfilefiname);
+   }
-   strcat(fileres,".txt");    /* Other files have txt extension */
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /*---------arguments file --------*/
+   fclose(ficrespop);
+ } /* End of popforecast */
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
+ int fileappend(FILE *fichier, char *optionfich)
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+ {
-     fflush(ficlog);
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-     goto end;
+     printf("Problem with file: %s\n", optionfich);
-   }
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
+   }
+   fflush(fichier);
-   strcpy(filereso,"o");
+   return (1);
-   strcat(filereso,fileres);
+ }
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     printf("Problem with Output resultfile: %s\n", filereso);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+ /**************** function prwizard **********************/
-     fflush(ficlog);
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-     goto end;
+ {
-   }
+   /* Wizard to print covariance matrix template */
-   /* Reads comments: lines beginning with '#' */
-   numlinepar=0;
+   char ca[32], cb[32];
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-     ungetc(c,ficpar);
+   int numlinepar;
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     puts(line);
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fputs(line,ficparo);
+   for(i=1; i <=nlstate; i++){
-     fputs(line,ficlog);
+     jj=0;
-   }
+     for(j=1; j <=nlstate+ndeath; j++){
-   ungetc(c,ficpar);
+       if(j==i) continue;
+       jj++;
-   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);
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   numlinepar++;
+       printf("%1d%1d",i,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);
+       fprintf(ficparo,"%1d%1d",i,j);
-   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);
+       for(k=1; k<=ncovmodel;k++){
-   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);
+         /*        printf(" %lf",param[i][j][k]); */
-   fflush(ficlog);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+         printf(" 0.");
-     ungetc(c,ficpar);
+         fprintf(ficparo," 0.");
-     fgets(line, MAXLINE, ficpar);
+       }
-     numlinepar++;
+       printf("\n");
-     puts(line);
+       fprintf(ficparo,"\n");
-     fputs(line,ficparo);
+     }
-     fputs(line,ficlog);
+   }
-   }
+   printf("# Scales (for hessian or gradient estimation)\n");
-   ungetc(c,ficpar);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
-   covar=matrix(0,NCOVMAX,1,n);
+     jj=0;
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+     for(j=1; j <=nlstate+ndeath; j++){
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       if(j==i) continue;
+       jj++;
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+       fprintf(ficparo,"%1d%1d",i,j);
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       printf("%1d%1d",i,j);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         /*      printf(" %le",delti3[i][j][k]); */
-   delti=delti3[1][1];
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+         printf(" 0.");
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+         fprintf(ficparo," 0.");
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+       }
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       numlinepar++;
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       printf("\n");
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       fprintf(ficparo,"\n");
-     fclose (ficparo);
+     }
-     fclose (ficlog);
+   }
-     goto end;
+   printf("# Covariance matrix\n");
-     exit(0);
+ /* # 121 Var(a12)\n\ */
-   }
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   else if(mle==-3) {
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-     matcov=matrix(1,npar,1,npar);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-   }
+   fflush(stdout);
-   else{
+   fprintf(ficparo,"# Covariance matrix\n");
-     /* Read guess parameters */
+   /* # 121 Var(a12)\n\ */
-     /* Reads comments: lines beginning with '#' */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   /* #   ...\n\ */
-       ungetc(c,ficpar);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-       fgets(line, MAXLINE, ficpar);
-       numlinepar++;
+   for(itimes=1;itimes<=2;itimes++){
-       puts(line);
+     jj=0;
-       fputs(line,ficparo);
+     for(i=1; i <=nlstate; i++){
-       fputs(line,ficlog);
+       for(j=1; j <=nlstate+ndeath; j++){
-     }
+         if(j==i) continue;
-     ungetc(c,ficpar);
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+           ca[0]= k+'a'-1;ca[1]='\0';
-     for(i=1; i <=nlstate; i++){
+           if(itimes==1){
-       j=0;
+             printf("#%1d%1d%d",i,j,k);
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-         if(jj==i) continue;
+           }else{
-         j++;
+             printf("%1d%1d%d",i,j,k);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-         if ((i1 != i) && (j1 != j)){
+             /*  printf(" %.5le",matcov[i][j]); */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+           }
- It might be a problem of design; if ncovcol and the model are correct\n \
+           ll=0;
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+           for(li=1;li <=nlstate; li++){
-           exit(1);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-         }
+               if(lj==li) continue;
-         fprintf(ficparo,"%1d%1d",i1,j1);
+               for(lk=1;lk<=ncovmodel;lk++){
-         if(mle==1)
+                 ll++;
-           printf("%1d%1d",i,j);
+                 if(ll<=jj){
-         fprintf(ficlog,"%1d%1d",i,j);
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-         for(k=1; k<=ncovmodel;k++){
+                   if(ll<jj){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+                     if(itimes==1){
-           if(mle==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-             printf(" %lf",param[i][j][k]);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-             fprintf(ficlog," %lf",param[i][j][k]);
+                     }else{
-           }
+                       printf(" 0.");
-           else
+                       fprintf(ficparo," 0.");
-             fprintf(ficlog," %lf",param[i][j][k]);
+                     }
-           fprintf(ficparo," %lf",param[i][j][k]);
+                   }else{
-         }
+                     if(itimes==1){
-         fscanf(ficpar,"\n");
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-         numlinepar++;
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-         if(mle==1)
+                     }else{
-           printf("\n");
+                       printf(" 0.");
-         fprintf(ficlog,"\n");
+                       fprintf(ficparo," 0.");
-         fprintf(ficparo,"\n");
+                     }
-       }
+                   }
-     }
+                 }
-     fflush(ficlog);
+               } /* end lk */
+             } /* end lj */
-     p=param[1][1];
+           } /* end li */
+           printf("\n");
-     /* Reads comments: lines beginning with '#' */
+           fprintf(ficparo,"\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           numlinepar++;
-       ungetc(c,ficpar);
+         } /* end k*/
-       fgets(line, MAXLINE, ficpar);
+       } /*end j */
-       numlinepar++;
+     } /* end i */
-       puts(line);
+   } /* end itimes */
-       fputs(line,ficparo);
-       fputs(line,ficlog);
+ } /* end of prwizard */
-     }
+ /******************* Gompertz Likelihood ******************************/
-     ungetc(c,ficpar);
+ double gompertz(double x[])
+ {
-     for(i=1; i <=nlstate; i++){
+   double A,B,L=0.0,sump=0.,num=0.;
-       for(j=1; j <=nlstate+ndeath-1; j++){
+   int i,n=0; /* n is the size of the sample */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+   for (i=0;i<=imx-1 ; i++) {
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+     sump=sump+weight[i];
-           exit(1);
+     /*    sump=sump+1;*/
-         }
+     num=num+1;
-         printf("%1d%1d",i,j);
+   }
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
+   /* for (i=0; i<=imx; i++)
-           fscanf(ficpar,"%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]);*/
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+   for (i=1;i<=imx ; i++)
-           fprintf(ficlog," %le",delti3[i][j][k]);
+     {
-         }
+       if (cens[i] == 1 && wav[i]>1)
-         fscanf(ficpar,"\n");
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-         numlinepar++;
-         printf("\n");
+       if (cens[i] == 0 && wav[i]>1)
-         fprintf(ficparo,"\n");
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-         fprintf(ficlog,"\n");
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-       }
-     }
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     fflush(ficlog);
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
-     delti=delti3[1][1];
+         /*      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 */
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     /* Reads comments: lines beginning with '#' */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   return -2*L*num/sump;
-       ungetc(c,ficpar);
+ }
-       fgets(line, MAXLINE, ficpar);
-       numlinepar++;
+ #ifdef GSL
-       puts(line);
+ /******************* Gompertz_f Likelihood ******************************/
-       fputs(line,ficparo);
+ double gompertz_f(const gsl_vector *v, void *params)
-       fputs(line,ficlog);
+ {
-     }
+   double A,B,LL=0.0,sump=0.,num=0.;
-     ungetc(c,ficpar);
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
-     matcov=matrix(1,npar,1,npar);
-     for(i=1; i <=npar; i++){
+   for (i=0;i<=imx-1 ; i++) {
-       fscanf(ficpar,"%s",&str);
+     sump=sump+weight[i];
-       if(mle==1)
+     /*    sump=sump+1;*/
-         printf("%s",str);
+     num=num+1;
-       fprintf(ficlog,"%s",str);
+   }
-       fprintf(ficparo,"%s",str);
-       for(j=1; j <=i; j++){
-         fscanf(ficpar," %le",&matcov[i][j]);
+   /* for (i=0; i<=imx; i++)
-         if(mle==1){
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-           printf(" %.5le",matcov[i][j]);
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-         }
+   for (i=1;i<=imx ; i++)
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     {
-         fprintf(ficparo," %.5le",matcov[i][j]);
+       if (cens[i] == 1 && wav[i]>1)
-       }
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       fscanf(ficpar,"\n");
-       numlinepar++;
+       if (cens[i] == 0 && wav[i]>1)
-       if(mle==1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-         printf("\n");
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-       fprintf(ficlog,"\n");
-       fprintf(ficparo,"\n");
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     }
+       if (wav[i] > 1 ) { /* ??? */
-     for(i=1; i <=npar; i++)
+         LL=LL+A*weight[i];
-       for(j=i+1;j<=npar;j++)
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-         matcov[i][j]=matcov[j][i];
+       }
+     }
-     if(mle==1)
-       printf("\n");
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     fprintf(ficlog,"\n");
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-     fflush(ficlog);
+   return -2*LL*num/sump;
+ }
-     /*-------- Rewriting parameter file ----------*/
+ #endif
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+ /******************* Printing html file ***********/
-     strcat(rfileres,".");    /* */
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+                   int lastpass, int stepm, int weightopt, char model[],\
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+                   int imx,  double p[],double **matcov,double agemortsup){
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+   int i,k;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     }
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     fprintf(ficres,"#%s\n",version);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   }    /* End of mle != -3 */
+   for (i=1;i<=2;i++)
+     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]));
-   /*-------- data file ----------*/
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   if((fic=fopen(datafile,"r"))==NULL)    {
+   fprintf(fichtm,"</ul>");
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   }
+  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>");
-   n= lastobs;
-   severity = vector(1,maxwav);
+  for (k=agegomp;k<(agemortsup-2);k++)
-   outcome=imatrix(1,maxwav+1,1,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]);
-   num=lvector(1,n);
-   moisnais=vector(1,n);
-   annais=vector(1,n);
+   fflush(fichtm);
-   moisdc=vector(1,n);
+ }
-   andc=vector(1,n);
-   agedc=vector(1,n);
+ /******************* Gnuplot file **************/
-   cod=ivector(1,n);
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   weight=vector(1,n);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   char dirfileres[132],optfileres[132];
-   mint=matrix(1,maxwav,1,n);
-   anint=matrix(1,maxwav,1,n);
+   int ng;
-   s=imatrix(1,maxwav+1,1,n);
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   i=1;
+     /*#endif */
-   linei=0;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     linei=linei+1;
+   strcpy(dirfileres,optionfilefiname);
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+   strcpy(optfileres,"vpl");
-       if(line[j] == '\t')
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-         line[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");
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   /* 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);
-     };
-     line[j+1]=0;  /* Trims blanks at end of line */
+ }
-     if(line[0]=='#'){
-       fprintf(ficlog,"Comment line\n%s\n",line);
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-       printf("Comment line\n%s\n",line);
+ {
-       continue;
-     }
+   /*-------- data file ----------*/
+   FILE *fic;
-     for (j=maxwav;j>=1;j--){
+   char dummy[]="                         ";
-       cutv(stra, strb,line,' ');
+   int i=0, j=0, n=0;
-       errno=0;
+   int linei, month, year,iout;
-       lval=strtol(strb,&endptr,10);
+   char line[MAXLINE], linetmp[MAXLINE];
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   char stra[MAXLINE], strb[MAXLINE];
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   char *stratrunc;
-         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);
+   int lstra;
-         exit(1);
-       }
-       s[j][i]=lval;
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-       strcpy(line,stra);
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       cutv(stra, strb,line,' ');
+   }
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       }
+   i=1;
-       else  if(iout=sscanf(strb,"%s.") != 0){
+   linei=0;
-         month=99;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-         year=9999;
+     linei=linei+1;
-       }else{
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-         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);
+       if(line[j] == '\t')
-         exit(1);
+         line[j] = ' ';
-       }
+     }
-       anint[j][i]= (double) year;
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       mint[j][i]= (double)month;
+       ;
-       strcpy(line,stra);
+     };
-     } /* ENd Waves */
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
-     cutv(stra, strb,line,' ');
+       fprintf(ficlog,"Comment line\n%s\n",line);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       printf("Comment line\n%s\n",line);
-     }
+       continue;
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+     }
-       month=99;
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       year=9999;
+     strcpy(line, linetmp);
-     }else{
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-       exit(1);
+     for (j=maxwav;j>=1;j--){
-     }
+       cutv(stra, strb, line, ' ');
-     andc[i]=(double) year;
+       if(strb[0]=='.') { /* Missing status */
-     moisdc[i]=(double) month;
+         lval=-1;
-     strcpy(line,stra);
+       }else{
+         errno=0;
-     cutv(stra, strb,line,' ');
+         lval=strtol(strb,&endptr,10);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     }
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     else  if(iout=sscanf(strb,"%s.") != 0){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-       month=99;
+           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);
-       year=9999;
+           return 1;
-     }else{
+         }
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+       }
-       exit(1);
+       s[j][i]=lval;
-     }
-     annais[i]=(double)(year);
+       strcpy(line,stra);
-     moisnais[i]=(double)(month);
+       cutv(stra, strb,line,' ');
-     strcpy(line,stra);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
+       }
-     cutv(stra, strb,line,' ');
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-     errno=0;
+         month=99;
-     dval=strtod(strb,&endptr);
+         year=9999;
-     if( strb[0]=='\0' || (*endptr != '\0')){
+       }else{
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+         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);
-       exit(1);
+         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);
-     }
+         return 1;
-     weight[i]=dval;
+       }
-     strcpy(line,stra);
+       anint[j][i]= (double) year;
+       mint[j][i]= (double)month;
-     for (j=ncovcol;j>=1;j--){
+       strcpy(line,stra);
-       cutv(stra, strb,line,' ');
+     } /* ENd Waves */
-       errno=0;
-       lval=strtol(strb,&endptr,10);
+     cutv(stra, strb,line,' ');
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+     }
-         exit(1);
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-       }
+       month=99;
-       if(lval <-1 || lval >1){
+       year=9999;
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+     }else{
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\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);
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\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);
-  For example, for multinomial values like 1, 2 and 3,\n \
+         return 1;
-  build V1=0 V2=0 for the reference value (1),\n \
+     }
-         V1=1 V2=0 for (2) \n \
+     andc[i]=(double) year;
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+     moisdc[i]=(double) month;
-  output of IMaCh is often meaningless.\n \
+     strcpy(line,stra);
-  Exiting.\n",lval,linei, i,line,j);
-         exit(1);
+     cutv(stra, strb,line,' ');
-       }
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-       covar[j][i]=(double)(lval);
+     }
-       strcpy(line,stra);
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-     }
+       month=99;
-     lstra=strlen(stra);
+       year=9999;
+     }else{
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       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);
-       stratrunc = &(stra[lstra-9]);
+       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);
-       num[i]=atol(stratrunc);
+         return 1;
      }
-     else
+     if (year==9999) {
-       num[i]=atol(stra);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+       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);
-       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;}*/
+         return 1;
-     i=i+1;
+     }
-   } /* End loop reading  data */
+     annais[i]=(double)(year);
-   fclose(fic);
+     moisnais[i]=(double)(month);
-   /* printf("ii=%d", ij);
+     strcpy(line,stra);
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
+     cutv(stra, strb,line,' ');
+     errno=0;
-   /* for (i=1; i<=imx; i++){
+     dval=strtod(strb,&endptr);
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+     if( strb[0]=='\0' || (*endptr != '\0')){
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+       printf("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[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-     }*/
+       fflush(ficlog);
-    /*  for (i=1; i<=imx; i++){
+       return 1;
-      if (s[4][i]==9)  s[4][i]=-1;
+     }
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+     weight[i]=dval;
+     strcpy(line,stra);
-   /* for (i=1; i<=imx; i++) */
+     for (j=ncovcol;j>=1;j--){
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+       cutv(stra, strb,line,' ');
-      else weight[i]=1;*/
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
-   /* Calculation of the number of parameters from char model */
+       }else{
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+         errno=0;
-   Tprod=ivector(1,15);
+         lval=strtol(strb,&endptr,10);
-   Tvaraff=ivector(1,15);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   Tvard=imatrix(1,15,1,2);
+           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);
-   Tage=ivector(1,15);
+           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);
+           return 1;
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+         }
-     j=0, j1=0, k1=1, k2=1;
+       }
-     j=nbocc(model,'+'); /* j=Number of '+' */
+       if(lval <-1 || lval >1){
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     cptcovn=j+1;
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     cptcovprod=j1; /*Number of products */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
-     strcpy(modelsav,model);
+  build V1=0 V2=0 for the reference value (1),\n \
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+         V1=1 V2=0 for (2) \n \
-       printf("Error. Non available option model=%s ",model);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+  output of IMaCh is often meaningless.\n \
-       goto end;
+  Exiting.\n",lval,linei, i,line,j);
-     }
+         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 \
-     /* This loop fills the array Tvar from the string 'model'.*/
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
-     for(i=(j+1); i>=1;i--){
+  build V1=0 V2=0 for the reference value (1),\n \
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+         V1=1 V2=0 for (2) \n \
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+  output of IMaCh is often meaningless.\n \
-       /*scanf("%d",i);*/
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       if (strchr(strb,'*')) {  /* Model includes a product */
+         return 1;
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+       }
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+       covar[j][i]=(double)(lval);
-           cptcovprod--;
+       strcpy(line,stra);
-           cutv(strb,stre,strd,'V');
+     }
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+     lstra=strlen(stra);
-           cptcovage++;
-             Tage[cptcovage]=i;
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-             /*printf("stre=%s ", stre);*/
+       stratrunc = &(stra[lstra-9]);
-         }
+       num[i]=atol(stratrunc);
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+     }
-           cptcovprod--;
+     else
-           cutv(strb,stre,strc,'V');
+       num[i]=atol(stra);
-           Tvar[i]=atoi(stre);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-           cptcovage++;
+       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;}*/
-           Tage[cptcovage]=i;
-         }
+     i=i+1;
-         else {  /* Age is not in the model */
+   } /* End loop reading  data */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
+   *imax=i-1; /* Number of individuals */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+   fclose(fic);
-           Tprod[k1]=i;
-           Tvard[k1][1]=atoi(strc); /* m*/
+   return (0);
-           Tvard[k1][2]=atoi(stre); /* n */
+   /* endread: */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+     printf("Exiting readdata: ");
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+     fclose(fic);
-           for (k=1; k<=lastobs;k++)
+     return (1);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           k1++;
-           k2=k2+2;
-         }
+ }
-       }
+ void removespace(char *str) {
-       else { /* no more sum */
+   char *p1 = str, *p2 = str;
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+   do
-        /*  scanf("%d",i);*/
+     while (*p2 == ' ')
-       cutv(strd,strc,strb,'V');
+       p2++;
-       Tvar[i]=atoi(strc);
+   while (*p1++ == *p2++);
-       }
+ }
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-         scanf("%d",i);*/
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-     } /* end of loop + */
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-   } /* end model */
+    * - cptcovn or number of covariates k of the models excluding age*products =6
+    * - cptcovage number of covariates with age*products =2
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+    * - cptcovs number of simple covariates
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+    *     which is a new column after the 9 (ncovcol) variables.
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-   printf("cptcovprod=%d ", cptcovprod);
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+    *    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 .
-   scanf("%d ",i);*/
+  */
+ {
-     /*  if(mle==1){*/
+   int i, j, k, ks;
-   if (weightopt != 1) { /* Maximisation without weights*/
+   int  j1, k1, k2;
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   char modelsav[80];
-   }
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-     /*-calculation of age at interview from date of interview and age at death -*/
-   agev=matrix(1,maxwav,1,imx);
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-   for (i=1; i<=imx; i++) {
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     for(m=2; (m<= maxwav); m++) {
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-         anint[m][i]=9999;
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-         s[m][i]=-1;
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-       }
+                   /* including age products which are counted in cptcovage.
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+                   * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-         nberr++;
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-         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);
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-         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);
+     strcpy(modelsav,model);
-         s[m][i]=-1;
+     if (strstr(model,"AGE") !=0){
-       }
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-         nberr++;
+       return 1;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+     }
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+     if (strstr(model,"v") !=0){
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       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++)  {
+     /*   Design
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-     for(m=firstpass; (m<= lastpass); m++){
+      *  <          ncovcol=8                >
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-         if (s[m][i] >= nlstate+1) {
+      *   k=  1    2      3       4     5       6      7        8
-           if(agedc[i]>0)
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-               agev[m][i]=agedc[i];
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-             else {
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-               if ((int)andc[i]!=9999){
+      *  Tage[++cptcovage]=k
-                 nbwarn++;
+      *       if products, new covar are created after ncovcol with k1
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-                 agev[m][i]=-1;
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
-               }
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-             }
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-         }
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+      *  <          ncovcol=8                >
-                                  years but with the precision of a month */
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-             agev[m][i]=1;
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-           else if(agev[m][i] <agemin){
+      * p Tprod[1]@2={                         6, 5}
-             agemin=agev[m][i];
+      *p Tvard[1][1]@4= {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);*/
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-           }
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           else if(agev[m][i] >agemax){
+      *How to reorganize?
-             agemax=agev[m][i];
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-           }
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+      * Struct []
-           /*     agev[m][i] = age[i]+2*m;*/
+      */
-         }
-         else { /* =9 */
+     /* This loop fills the array Tvar from the string 'model'.*/
-           agev[m][i]=1;
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-           s[m][i]=-1;
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-         }
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-       }
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-       else /*= 0 Unknown */
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-         agev[m][i]=1;
+     /*  k=1 Tvar[1]=2 (from V2) */
-     }
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
-   }
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-   for (i=1; i<=imx; i++)  {
+     /*  } */
-     for(m=firstpass; (m<=lastpass); m++){
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       if (s[m][i] > (nlstate+ndeath)) {
+     /*
-         nberr++;
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-         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);
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-         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);
+         Tvar[k]=0;
-         goto end;
+     cptcovage=0;
-       }
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-     }
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-   }
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-   /*for (i=1; i<=imx; i++){
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-   for (m=firstpass; (m<lastpass); m++){
+       /*scanf("%d",i);*/
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
- }
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
- }*/
+           /* covar is not filled and then is empty */
+           cptcovprod--;
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           cptcovage++; /* Sums the number of covariates which include age as a product */
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-   agegomp=(int)agemin;
+           /*printf("stre=%s ", stre);*/
-   free_vector(severity,1,maxwav);
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-   free_imatrix(outcome,1,maxwav+1,1,n);
+           cptcovprod--;
-   free_vector(moisnais,1,n);
+           cutl(stre,strb,strc,'V');
-   free_vector(annais,1,n);
+           Tvar[k]=atoi(stre);
-   /* free_matrix(mint,1,maxwav,1,n);
+           cptcovage++;
-      free_matrix(anint,1,maxwav,1,n);*/
+           Tage[cptcovage]=k;
-   free_vector(moisdc,1,n);
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-   free_vector(andc,1,n);
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+           cptcovn++;
+           cptcovprodnoage++;k1++;
-   wav=ivector(1,imx);
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+                                   because this model-covariate is a construction we invent a new column
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+                                   ncovcol + k1
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-   /* Concatenates waves */
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+           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  */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-   Tcode=ivector(1,100);
+           k2=k2+2;
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-   ncodemax[1]=1;
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+           for (i=1; i<=lastobs;i++){
+             /* Computes the new covariate which is a product of
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-                                  the estimations*/
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-   h=0;
+           }
-   m=pow(2,cptcoveff);
+         } /* End age is not in the model */
+       } /* End if model includes a product */
-   for(k=1;k<=cptcoveff; k++){
+       else { /* no more sum */
-     for(i=1; i <=(m/pow(2,k));i++){
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       for(j=1; j <= ncodemax[k]; j++){
+        /*  scanf("%d",i);*/
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         cutl(strd,strc,strb,'V');
-           h++;
+         ks++; /**< Number of simple covariates */
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+         cptcovn++;
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+         Tvar[k]=atoi(strd);
-         }
+       }
-       }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-     }
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-   }
+         scanf("%d",i);*/
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+     } /* end of loop + */
-      codtab[1][2]=1;codtab[2][2]=2; */
+   } /* end model */
-   /* for(i=1; i <=m ;i++){
-      for(k=1; k <=cptcovn; k++){
+   /*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("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-      }
-      printf("\n");
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-      }
+   printf("cptcovprod=%d ", cptcovprod);
-      scanf("%d",i);*/
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   /*------------ gnuplot -------------*/
+   scanf("%d ",i);*/
-   strcpy(optionfilegnuplot,optionfilefiname);
-   if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-   strcat(optionfilegnuplot,".gp");
+   /*endread:*/
+     printf("Exiting decodemodel: ");
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     return (1);
-     printf("Problem with file %s",optionfilegnuplot);
+ }
-   }
-   else{
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-     fprintf(ficgp,"\n# %s\n", version);
+ {
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   int i, m;
-     fprintf(ficgp,"set missing 'NaNq'\n");
-   }
+   for (i=1; i<=imx; i++) {
-   /*  fclose(ficgp);*/
+     for(m=2; (m<= maxwav); m++) {
-   /*--------- index.htm --------*/
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+         s[m][i]=-1;
-   if(mle==-3)
+       }
-     strcat(optionfilehtm,"-mort");
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-   strcat(optionfilehtm,".htm");
+         *nberr = *nberr + 1;
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+         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);
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
-   }
+         s[m][i]=-1;
+       }
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-   strcat(optionfilehtmcov,"-cov.htm");
+         (*nberr)++;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+         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]);
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-   }
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-   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);
+   for (i=1; i<=imx; i++)  {
-   }
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         if (s[m][i] >= nlstate+1) {
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+           if(agedc[i]>0){
- \n\
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
- <hr  size=\"2\" color=\"#EC5E5E\">\
+               agev[m][i]=agedc[i];
-  <ul><li><h4>Parameter files</h4>\n\
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+             }else {
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+               if ((int)andc[i]!=9999){
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+                 nbwarn++;
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-  - Date and time at start: %s</ul>\n",\
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+                 agev[m][i]=-1;
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+               }
-           fileres,fileres,\
+             }
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+           } /* agedc > 0 */
-   fflush(fichtm);
+         }
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-   strcpy(pathr,path);
+                                  years but with the precision of a month */
-   strcat(pathr,optionfilefiname);
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+           else if(agev[m][i] < *agemin){
-      and prints on file fileres'p'. */
+             *agemin=agev[m][i];
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
-   fprintf(fichtm,"\n");
+           else if(agev[m][i] >*agemax){
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+             *agemax=agev[m][i];
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           }
-           imx,agemin,agemax,jmin,jmax,jmean);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           /*     agev[m][i] = age[i]+2*m;*/
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         }
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         else { /* =9 */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           agev[m][i]=1;
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+           s[m][i]=-1;
+         }
+       }
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       else /*= 0 Unknown */
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+         agev[m][i]=1;
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+     }
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   }
+   for (i=1; i<=imx; i++)  {
-   if (mle==-3){
+     for(m=firstpass; (m<=lastpass); m++){
-     ximort=matrix(1,NDIM,1,NDIM);
+       if (s[m][i] > (nlstate+ndeath)) {
-     cens=ivector(1,n);
+         (*nberr)++;
-     ageexmed=vector(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);
-     agecens=vector(1,n);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-     dcwave=ivector(1,n);
+         return 1;
+       }
-     for (i=1; i<=imx; i++){
+     }
-       dcwave[i]=-1;
+   }
-       for (m=firstpass; m<=lastpass; m++)
-         if (s[m][i]>nlstate) {
+   /*for (i=1; i<=imx; i++){
-           dcwave[i]=m;
+   for (m=firstpass; (m<lastpass); m++){
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-           break;
+ }
-         }
-     }
+ }*/
-     for (i=1; i<=imx; i++) {
-       if (wav[i]>0){
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         ageexmed[i]=agev[mw[1][i]][i];
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         j=wav[i];
-         agecens[i]=1.;
+   return (0);
+  /* endread:*/
-         if (ageexmed[i]> 1 && wav[i] > 0){
+     printf("Exiting calandcheckages: ");
-           agecens[i]=agev[mw[j][i]][i];
+     return (1);
-           cens[i]= 1;
+ }
-         }else if (ageexmed[i]< 1)
-           cens[i]= -1;
+ void syscompilerinfo()
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+  {
-           cens[i]=0 ;
+    /* #include "syscompilerinfo.h"*/
-       }
+    /* #include <gnu/libc-version.h> */ /* Only on gnu */
-       else cens[i]=-1;
+ #include <stdint.h>
-     }
+    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
-     for (i=1;i<=NDIM;i++) {
+    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
-       for (j=1;j<=NDIM;j++)
+ #endif
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
-     }
+    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
-     p[1]=0.0268; p[NDIM]=0.083;
+ #if defined(__GNUC__) || defined(__GNUG__)
-     /*printf("%lf %lf", p[1], p[2]);*/
+    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
-     strcpy(filerespow,"pow-mort");
+ #endif
-     strcat(filerespow,fileres);
+ #if defined(__IBMC__) || defined(__IBMCPP__)
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
-       printf("Problem with resultfile: %s\n", filerespow);
+ #endif
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ #if defined(_MSC_VER)
-     }
+    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
-     /*  for (i=1;i<=nlstate;i++)
+ #if defined(__PGI)
-         for(j=1;j<=nlstate+ndeath;j++)
+    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+ #endif
-     */
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-     fprintf(ficrespow,"\n");
+    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+    printf(". ");fprintf(ficlog,". ");
-     fclose(ficrespow);
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
+     // Windows (x64 and x86)
-     for(i=1; i <=NDIM; i++)
+ #elif __unix__ // all unices, not all compilers
-       for(j=i+1;j<=NDIM;j++)
+     // Unix
-         matcov[i][j]=matcov[j][i];
+ #elif __linux__
+     // linux
-     printf("\nCovariance matrix\n ");
+ #elif __APPLE__
-     for(i=1; i <=NDIM; i++) {
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
-       for(j=1;j<=NDIM;j++){
+ #endif
-         printf("%f ",matcov[i][j]);
-       }
+ /*  __MINGW32__   */
-       printf("\n ");
+ /*  __CYGWIN__   */
-     }
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
-     for (i=1;i<=NDIM;i++)
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ /* _WIN64  // Defined for applications for Win64. */
+ /* _M_X64 // Defined for compilations that target x64 processors. */
-     lsurv=vector(1,AGESUP);
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
-     lpop=vector(1,AGESUP);
-     tpop=vector(1,AGESUP);
+ #if UINTPTR_MAX == 0xffffffff
-     lsurv[agegomp]=100000;
+    printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
-     for (k=agegomp;k<=AGESUP;k++) {
+    printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
-       agemortsup=k;
+ #else
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+    printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
-     }
+ #endif
-     for (k=agegomp;k<agemortsup;k++)
+ /* struct utsname sysInfo;
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+    if (uname(&sysInfo) != -1) {
-     for (k=agegomp;k<agemortsup;k++){
+      printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+      fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       sumlpop=sumlpop+lpop[k];
+    }
-     }
+    else
+       perror("uname() error");
-     tpop[agegomp]=sumlpop;
+           */
-     for (k=agegomp;k<(agemortsup-3);k++){
+ #if defined(__GNUC__)
-       /*  tpop[k+1]=2;*/
+ # if defined(__GNUC_PATCHLEVEL__)
-       tpop[k+1]=tpop[k]-lpop[k];
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     }
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     for (k=agegomp;k<(agemortsup-2);k++)
+                             + __GNUC_MINOR__ * 100)
-       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]);
+ # endif
+    printf("GNU C version %d.\n", __GNUC_VERSION__);
+    fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ #endif
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ #if defined(_MSC_VER)
+    /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+    /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-                      stepm, weightopt,\
+ #endif
-                      model,imx,p,matcov,agemortsup);
+   /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
-     free_vector(lsurv,1,AGESUP);
-     free_vector(lpop,1,AGESUP);
+  }
-     free_vector(tpop,1,AGESUP);
-   } /* Endof if mle==-3 */
+ /***********************************************/
+ /**************** Main Program *****************/
-   else{ /* For mle >=1 */
+ /***********************************************/
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ int main(int argc, char *argv[])
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+ {
-     for (k=1; k<=npar;k++)
+ #ifdef GSL
-       printf(" %d %8.5f",k,p[k]);
+   const gsl_multimin_fminimizer_type *T;
-     printf("\n");
+   size_t iteri = 0, it;
-     globpr=1; /* to print the contributions */
+   int rval = GSL_CONTINUE;
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   int status = GSL_SUCCESS;
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   double ssval;
-     for (k=1; k<=npar;k++)
+ #endif
-       printf(" %d %8.5f",k,p[k]);
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-     printf("\n");
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     if(mle>=1){ /* Could be 1 or 2 */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+   int jj, ll, li, lj, lk;
-     }
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
-     /*--------- results files --------------*/
+   int NDIM=2;
-     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);
+   int vpopbased=0;
+   char ca[32], cb[32];
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /*  FILE *fichtm; *//* Html File */
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /* FILE *ficgp;*/ /*Gnuplot File */
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   struct stat info;
-     for(i=1,jk=1; i <=nlstate; i++){
+   double agedeb;
-       for(k=1; k <=(nlstate+ndeath); k++){
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-         if (k != i) {
-           printf("%d%d ",i,k);
+   double fret;
-           fprintf(ficlog,"%d%d ",i,k);
+   double dum; /* Dummy variable */
-           fprintf(ficres,"%1d%1d ",i,k);
+   double ***p3mat;
-           for(j=1; j <=ncovmodel; j++){
+   double ***mobaverage;
-             printf("%lf ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+   char line[MAXLINE];
-             fprintf(ficres,"%lf ",p[jk]);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-             jk++;
+   char pathr[MAXLINE], pathimach[MAXLINE];
-           }
+   char *tok, *val; /* pathtot */
-           printf("\n");
+   int firstobs=1, lastobs=10;
-           fprintf(ficlog,"\n");
+   int c,  h , cpt;
-           fprintf(ficres,"\n");
+   int jl;
-         }
+   int i1, j1, jk, stepsize;
-       }
+   int *tab;
-     }
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     if(mle!=0){
+   int mobilav=0,popforecast=0;
-       /* Computing hessian and covariance matrix */
+   int hstepm, nhstepm;
-       ftolhess=ftol; /* Usually correct */
+   int agemortsup;
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+   float  sumlpop=0.;
-     }
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-     printf("# Scales (for hessian or gradient estimation)\n");
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   double bage=0, fage=110, age, agelim, agebase;
-     for(i=1,jk=1; i <=nlstate; i++){
+   double ftolpl=FTOL;
-       for(j=1; j <=nlstate+ndeath; j++){
+   double **prlim;
-         if (j!=i) {
+   double ***param; /* Matrix of parameters */
-           fprintf(ficres,"%1d%1d",i,j);
+   double  *p;
-           printf("%1d%1d",i,j);
+   double **matcov; /* Matrix of covariance */
-           fprintf(ficlog,"%1d%1d",i,j);
+   double ***delti3; /* Scale */
-           for(k=1; k<=ncovmodel;k++){
+   double *delti; /* Scale */
-             printf(" %.5e",delti[jk]);
+   double ***eij, ***vareij;
-             fprintf(ficlog," %.5e",delti[jk]);
+   double **varpl; /* Variances of prevalence limits by age */
-             fprintf(ficres," %.5e",delti[jk]);
+   double *epj, vepp;
-             jk++;
-           }
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-           printf("\n");
+   double **ximort;
-           fprintf(ficlog,"\n");
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-           fprintf(ficres,"\n");
+   int *dcwave;
-         }
-       }
+   char z[1]="c";
-     }
+   /*char  *strt;*/
-     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");
+   char strtend[80];
-     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");
+ /*   setlocale (LC_ALL, ""); */
-     /* # 121 Var(a12)\n\ */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /*   textdomain (PACKAGE); */
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /*   setlocale (LC_CTYPE, ""); */
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /*   setlocale (LC_MESSAGES, ""); */
-     /* # 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\ */
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+   rstart_time = time(NULL);
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
-     /* Just to have a covariance matrix which will be more understandable
+   /*tml = *localtime(&start_time.tm_sec);*/
-        even is we still don't want to manage dictionary of variables
+   /* strcpy(strstart,asctime(&tml)); */
-     */
+   strcpy(strstart,asctime(&start_time));
-     for(itimes=1;itimes<=2;itimes++){
-       jj=0;
+ /*  printf("Localtime (at start)=%s",strstart); */
-       for(i=1; i <=nlstate; i++){
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-         for(j=1; j <=nlstate+ndeath; j++){
+ /*  tm = *localtime(&start_time.tm_sec); */
-           if(j==i) continue;
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-           for(k=1; k<=ncovmodel;k++){
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-             jj++;
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-             ca[0]= k+'a'-1;ca[1]='\0';
+ /*   tp.tm_sec = mktime(&tmg); */
-             if(itimes==1){
+ /*   strt=asctime(&tmg); */
-               if(mle>=1)
+ /*   printf("Time(after) =%s",strstart);  */
-                 printf("#%1d%1d%d",i,j,k);
+ /*  (void) time (&time_value);
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+ *  tm = *localtime(&time_value);
-             }else{
+ *  strstart=asctime(&tm);
-               if(mle>=1)
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-                 printf("%1d%1d%d",i,j,k);
+ */
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+   nberr=0; /* Number of errors and warnings */
-             }
+   nbwarn=0;
-             ll=0;
+   getcwd(pathcd, size);
-             for(li=1;li <=nlstate; li++){
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+   printf("\n%s\n%s",version,fullversion);
-                 if(lj==li) continue;
+   if(argc <=1){
-                 for(lk=1;lk<=ncovmodel;lk++){
+     printf("\nEnter the parameter file name: ");
-                   ll++;
+     fgets(pathr,FILENAMELENGTH,stdin);
-                   if(ll<=jj){
+     i=strlen(pathr);
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+     if(pathr[i-1]=='\n')
-                     if(ll<jj){
+       pathr[i-1]='\0';
-                       if(itimes==1){
+     i=strlen(pathr);
-                         if(mle>=1)
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+       pathr[i-1]='\0';
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+    for (tok = pathr; tok != NULL; ){
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+       printf("Pathr |%s|\n",pathr);
-                       }else{
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-                         if(mle>=1)
+       printf("val= |%s| pathr=%s\n",val,pathr);
-                           printf(" %.5e",matcov[jj][ll]);
+       strcpy (pathtot, val);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+       if(pathr[0] == '\0') break; /* Dirty */
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+     }
-                       }
+   }
-                     }else{
+   else{
-                       if(itimes==1){
+     strcpy(pathtot,argv[1]);
-                         if(mle>=1)
+   }
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+   /*cygwin_split_path(pathtot,path,optionfile);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-                       }else{
+   /* cutv(path,optionfile,pathtot,'\\');*/
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+   /* Split argv[0], imach program to get pathimach */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-                       }
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-                     }
+  /*   strcpy(pathimach,argv[0]); */
-                   }
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-                 } /* end lk */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-               } /* end lj */
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-             } /* end li */
+   chdir(path); /* Can be a relative path */
-             if(mle>=1)
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-               printf("\n");
+     printf("Current directory %s!\n",pathcd);
-             fprintf(ficlog,"\n");
+   strcpy(command,"mkdir ");
-             fprintf(ficres,"\n");
+   strcat(command,optionfilefiname);
-             numlinepar++;
+   if((outcmd=system(command)) != 0){
-           } /* end k*/
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
-         } /*end j */
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-       } /* end i */
+     /* fclose(ficlog); */
-     } /* end itimes */
+ /*     exit(1); */
+   }
-     fflush(ficlog);
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-     fflush(ficres);
+ /*     perror("mkdir"); */
+ /*   } */
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   /*-------- arguments in the command line --------*/
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+   /* Log file */
-       fputs(line,ficparo);
+   strcat(filelog, optionfilefiname);
-     }
+   strcat(filelog,".log");    /* */
-     ungetc(c,ficpar);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
-     estepm=0;
+     goto end;
-     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;
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     if (fage <= 2) {
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-       bage = ageminpar;
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-       fage = agemaxpar;
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     }
+  path=%s \n\
+  optionfile=%s\n\
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+  optionfilext=%s\n\
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   syscompilerinfo();
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   printf("Local time (at start):%s",strstart);
-       fgets(line, MAXLINE, ficpar);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-       puts(line);
+   fflush(ficlog);
-       fputs(line,ficparo);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     }
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     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);
+   strcpy(fileres,"r");
-     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);
+   strcat(fileres, optionfilefiname);
-     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);
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     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);
+   /*---------arguments file --------*/
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-       ungetc(c,ficpar);
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-       fgets(line, MAXLINE, ficpar);
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-       puts(line);
+     fflush(ficlog);
-       fputs(line,ficparo);
+     /* goto end; */
-     }
+     exit(70);
-     ungetc(c,ficpar);
+   }
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+   strcpy(filereso,"o");
+   strcat(filereso,fileres);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+     printf("Problem with Output resultfile: %s\n", filereso);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     goto end;
-       ungetc(c,ficpar);
+   }
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+   /* Reads comments: lines beginning with '#' */
-       fputs(line,ficparo);
+   numlinepar=0;
-     }
+   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
+     fgets(line, MAXLINE, 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);
+     numlinepar++;
-     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);
+     fputs(line,stdout);
-     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);
+     fputs(line,ficparo);
-     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);
+     fputs(line,ficlog);
-     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.*/
+   ungetc(c,ficpar);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   numlinepar++;
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+   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);
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   fflush(ficlog);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     fgets(line, MAXLINE, ficpar);
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+     numlinepar++;
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     fputs(line, stdout);
+     //puts(line);
-    /*------------ free_vector  -------------*/
+     fputs(line,ficparo);
-    /*  chdir(path); */
+     fputs(line,ficlog);
+   }
-     free_ivector(wav,1,imx);
+   ungetc(c,ficpar);
-     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);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-     free_lvector(num,1,n);
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-     free_vector(agedc,1,n);
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+      v1+v2*age+v2*v3 makes cptcovn = 3
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   */
-     fclose(ficparo);
+   if (strlen(model)>1)
-     fclose(ficres);
+     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*/
+   else
+     ncovmodel=2;
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-     strcpy(filerespl,"pl");
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-     strcat(filerespl,fileres);
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     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);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     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);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     fflush(stdout);
-     }
+     fclose (ficlog);
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     goto end;
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   }
-     pstamp(ficrespl);
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+   delti=delti3[1][1];
-     fprintf(ficrespl,"#Age ");
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     fprintf(ficrespl,"\n");
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     prlim=matrix(1,nlstate,1,nlstate);
+     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);
-     agebase=ageminpar;
+     fclose (ficparo);
-     agelim=agemaxpar;
+     fclose (ficlog);
-     ftolpl=1.e-10;
+     goto end;
-     i1=cptcoveff;
+     exit(0);
-     if (cptcovn < 1){i1=1;}
+   }
+   else if(mle==-3) {
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-         k=k+1;
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-         fprintf(ficrespl,"\n#******");
+     matcov=matrix(1,npar,1,npar);
-         printf("\n#******");
+   }
-         fprintf(ficlog,"\n#******");
+   else{
-         for(j=1;j<=cptcoveff;j++) {
+     /* Read guessed parameters */
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     /* Reads comments: lines beginning with '#' */
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       ungetc(c,ficpar);
-         }
+       fgets(line, MAXLINE, ficpar);
-         fprintf(ficrespl,"******\n");
+       numlinepar++;
-         printf("******\n");
+       fputs(line,stdout);
-         fprintf(ficlog,"******\n");
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-         for (age=agebase; age<=agelim; age++){
+     }
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     ungetc(c,ficpar);
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(i=1; i <=nlstate; i++){
-           for(i=1; i<=nlstate;i++)
+       j=0;
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-           fprintf(ficrespl,"\n");
+         if(jj==i) continue;
-         }
+         j++;
-       }
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     }
+         if ((i1 != i) && (j1 != j)){
-     fclose(ficrespl);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
-     /*------------- h Pij x at various ages ------------*/
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+           exit(1);
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+         }
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+         fprintf(ficparo,"%1d%1d",i1,j1);
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+         if(mle==1)
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+           printf("%1d%1d",i,j);
-     }
+         fprintf(ficlog,"%1d%1d",i,j);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+         for(k=1; k<=ncovmodel;k++){
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+             printf(" %lf",param[i][j][k]);
-     /*if (stepm<=24) stepsize=2;*/
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
-     agelim=AGESUP;
+           else
-     hstepm=stepsize*YEARM; /* Every year of age */
+             fprintf(ficlog," %lf",param[i][j][k]);
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
-     /* hstepm=1;   aff par mois*/
+         fscanf(ficpar,"\n");
-     pstamp(ficrespij);
+         numlinepar++;
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+         if(mle==1)
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+           printf("\n");
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         fprintf(ficlog,"\n");
-         k=k+1;
+         fprintf(ficparo,"\n");
-         fprintf(ficrespij,"\n#****** ");
+       }
-         for(j=1;j<=cptcoveff;j++)
+     }
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fflush(ficlog);
-         fprintf(ficrespij,"******\n");
+     /* Reads scales values */
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+     p=param[1][1];
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       numlinepar++;
-           oldm=oldms;savm=savms;
+       fputs(line,stdout);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fputs(line,ficparo);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+       fputs(line,ficlog);
-           for(i=1; i<=nlstate;i++)
+     }
-             for(j=1; j<=nlstate+ndeath;j++)
+     ungetc(c,ficpar);
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
+     for(i=1; i <=nlstate; i++){
-           for (h=0; h<=nhstepm; h++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-             for(i=1; i<=nlstate;i++)
+         if ( (i1-i) * (j1-j) != 0){
-               for(j=1; j<=nlstate+ndeath;j++)
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           exit(1);
-             fprintf(ficrespij,"\n");
+         }
-           }
+         printf("%1d%1d",i,j);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-           fprintf(ficrespij,"\n");
+         fprintf(ficlog,"%1d%1d",i1,j1);
-         }
+         for(k=1; k<=ncovmodel;k++){
-       }
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-     }
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
-     fclose(ficrespij);
+         fscanf(ficpar,"\n");
+         numlinepar++;
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         printf("\n");
-     for(i=1;i<=AGESUP;i++)
+         fprintf(ficparo,"\n");
-       for(j=1;j<=NCOVMAX;j++)
+         fprintf(ficlog,"\n");
-         for(k=1;k<=NCOVMAX;k++)
+       }
-           probs[i][j][k]=0.;
+     }
+     fflush(ficlog);
-     /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     /* Reads covariance matrix */
-     if(prevfcast==1){
+     delti=delti3[1][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);*/
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-       /*      }  */
-       /*      else{ */
+     /* Reads comments: lines beginning with '#' */
-       /*        erreur=108; */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       /*        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); */
+       ungetc(c,ficpar);
-       /*        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); */
+       fgets(line, MAXLINE, ficpar);
-       /*      } */
+       numlinepar++;
-     }
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-     /*---------- Health expectancies and variances ------------*/
+     }
+     ungetc(c,ficpar);
-     strcpy(filerest,"t");
-     strcat(filerest,fileres);
+     matcov=matrix(1,npar,1,npar);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+     for(i=1; i <=npar; i++)
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-     }
+     for(i=1; i <=npar; i++){
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       fscanf(ficpar,"%s",str);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       if(mle==1)
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
-     strcpy(filerese,"e");
+       fprintf(ficparo,"%s",str);
-     strcat(filerese,fileres);
+       for(j=1; j <=i; j++){
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+         fscanf(ficpar," %le",&matcov[i][j]);
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+         if(mle==1){
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+           printf(" %.5le",matcov[i][j]);
-     }
+         }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
-     strcpy(fileresstde,"stde");
+       fscanf(ficpar,"\n");
-     strcat(fileresstde,fileres);
+       numlinepar++;
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       if(mle==1)
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+         printf("\n");
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"\n");
-     }
+       fprintf(ficparo,"\n");
-     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);
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
-     strcpy(filerescve,"cve");
+         matcov[i][j]=matcov[j][i];
-     strcat(filerescve,fileres);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+     if(mle==1)
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       printf("\n");
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     fprintf(ficlog,"\n");
-     }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fflush(ficlog);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     /*-------- Rewriting parameter file ----------*/
-     strcpy(fileresv,"v");
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(fileresv,fileres);
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     strcat(rfileres,".");    /* */
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-     }
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     }
+     fprintf(ficres,"#%s\n",version);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+   }    /* End of mle != -3 */
-     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);
+   n= lastobs;
-     */
+   num=lvector(1,n);
+   moisnais=vector(1,n);
-     if (mobilav!=0) {
+   annais=vector(1,n);
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   moisdc=vector(1,n);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   andc=vector(1,n);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   agedc=vector(1,n);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   cod=ivector(1,n);
-       }
+   weight=vector(1,n);
-     }
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   mint=matrix(1,maxwav,1,n);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   anint=matrix(1,maxwav,1,n);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-         k=k+1;
+   tab=ivector(1,NCOVMAX);
-         fprintf(ficrest,"\n#****** ");
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   /* Reads data from file datafile */
-         fprintf(ficrest,"******\n");
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
+     goto end;
-         fprintf(ficreseij,"\n#****** ");
-         fprintf(ficresstdeij,"\n#****** ");
+   /* Calculation of the number of parameters from char model */
-         fprintf(ficrescveij,"\n#****** ");
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-         for(j=1;j<=cptcoveff;j++) {
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         k=1 Tvar[1]=2 (from V2)
-         }
+     */
-         fprintf(ficreseij,"******\n");
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-         fprintf(ficresstdeij,"******\n");
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-         fprintf(ficrescveij,"******\n");
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
-         fprintf(ficresvij,"\n#****** ");
+   */
-         for(j=1;j<=cptcoveff;j++)
+   /* For model-covariate k tells which data-covariate to use but
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     because this model-covariate is a construction we invent a new column
-         fprintf(ficresvij,"******\n");
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     Tvar[3=V1*V4]=4+1 etc */
-         oldm=oldms;savm=savms;
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-         oldm=oldms;savm=savms;
+   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
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-         if(popbased==1){
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-         }
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-         pstamp(ficrest);
+                       */
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+   if(decodemodel(model, lastobs) == 1)
-         fprintf(ficrest,"\n");
+     goto end;
-         epj=vector(1,nlstate+1);
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-         for(age=bage; age <=fage ;age++){
+     nbwarn++;
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     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);
-           if (popbased==1) {
+     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(mobilav ==0){
+   }
-               for(i=1; i<=nlstate;i++)
+     /*  if(mle==1){*/
-                 prlim[i][i]=probs[(int)age][i][k];
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-             }else{ /* mobilav */
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-               for(i=1; i<=nlstate;i++)
+   }
-                 prlim[i][i]=mobaverage[(int)age][i][k];
-             }
+     /*-calculation of age at interview from date of interview and age at death -*/
-           }
+   agev=matrix(1,maxwav,1,imx);
-           fprintf(ficrest," %4.0f",age);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     goto end;
-             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]);*/
+   agegomp=(int)agemin;
-             }
+   free_vector(moisnais,1,n);
-             epj[nlstate+1] +=epj[j];
+   free_vector(annais,1,n);
-           }
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   free_vector(moisdc,1,n);
-             for(j=1;j <=nlstate;j++)
+   free_vector(andc,1,n);
-               vepp += vareij[i][j][(int)age];
+   /* */
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-           for(j=1;j <=nlstate;j++){
+   wav=ivector(1,imx);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-           }
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-           fprintf(ficrest,"\n");
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-         }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   /* Concatenates waves */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-         free_vector(epj,1,nlstate+1);
+   /* */
-       }
-     }
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     free_vector(weight,1,n);
-     free_imatrix(Tvard,1,15,1,2);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-     free_imatrix(s,1,maxwav+1,1,n);
+   ncodemax[1]=1;
-     free_matrix(anint,1,maxwav,1,n);
+   Ndum =ivector(-1,NCOVMAX);
-     free_matrix(mint,1,maxwav,1,n);
+   if (ncovmodel > 2)
-     free_ivector(cod,1,n);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-     free_ivector(tab,1,NCOVMAX);
-     fclose(ficreseij);
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-     fclose(ficresstdeij);
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-     fclose(ficrescveij);
+   h=0;
-     fclose(ficresvij);
-     fclose(ficrest);
-     fclose(ficpar);
+   /*if (cptcovn > 0) */
-     /*------- Variance of period (stable) prevalence------*/
+   m=pow(2,cptcoveff);
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     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("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-       exit(0);
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-     }
+           h++;
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+           if (h>m)
+             h=1;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+            *     h     1     2     3     4
-         k=k+1;
+            *______________________________
-         fprintf(ficresvpl,"\n#****** ");
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-         for(j=1;j<=cptcoveff;j++)
+            *     2     2     1     1     1
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     3 i=2 1     2     1     1
-         fprintf(ficresvpl,"******\n");
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+            *     6     2     1     2     1
-         oldm=oldms;savm=savms;
+            *     7 i=4 1     2     2     1
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+            *     8     2     2     2     1
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+            *     9 i=5 1 i=3 1 i=2 1     1
-       }
+            *    10     2     1     1     1
-     }
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
-     fclose(ficresvpl);
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
-     /*---------- End : free ----------------*/
+            *    15 i=8 1     2     2     1
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+            *    16     2     2     2     1
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+            */
+           codtab[h][k]=j;
-   }  /* mle==-3 arrives here for freeing */
+           /*codtab[h][Tvar[k]]=j;*/
-   free_matrix(prlim,1,nlstate,1,nlstate);
+           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]]);
-     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);
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-     free_matrix(matcov,1,npar,1,npar);
+      codtab[1][2]=1;codtab[2][2]=2; */
-     /*free_vector(delti,1,npar);*/
+   /* for(i=1; i <=m ;i++){
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+      for(k=1; k <=cptcovn; k++){
-     free_matrix(agev,1,maxwav,1,imx);
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+      }
+      printf("\n");
-     free_ivector(ncodemax,1,8);
+      }
-     free_ivector(Tvar,1,15);
+      scanf("%d",i);*/
-     free_ivector(Tprod,1,15);
-     free_ivector(Tvaraff,1,15);
+  free_ivector(Ndum,-1,NCOVMAX);
-     free_ivector(Tage,1,15);
-     free_ivector(Tcode,1,100);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   /*------------ gnuplot -------------*/
-     free_imatrix(codtab,1,100,1,10);
+   strcpy(optionfilegnuplot,optionfilefiname);
-   fflush(fichtm);
+   if(mle==-3)
-   fflush(ficgp);
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
-   if((nberr >0) || (nbwarn>0)){
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     printf("Problem with file %s",optionfilegnuplot);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }
-   }else{
+   else{
-     printf("End of Imach\n");
+     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficlog,"End of Imach\n");
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-   }
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-   printf("See log file on %s\n",filelog);
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   }
-   (void) gettimeofday(&end_time,&tzp);
+   /*  fclose(ficgp);*/
-   tm = *localtime(&end_time.tv_sec);
+   /*--------- index.htm --------*/
-   tmg = *gmtime(&end_time.tv_sec);
-   strcpy(strtend,asctime(&tm));
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   if(mle==-3)
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     strcat(optionfilehtm,"-mort");
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     printf("Problem with %s \n",optionfilehtm);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     exit(0);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   }
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   strcat(optionfilehtmcov,"-cov.htm");
-   fclose(fichtm);
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-   fclose(fichtmcov);
+   }
-   fclose(ficgp);
+   else{
-   fclose(ficlog);
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-   /*------ End -----------*/
+ <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);
-    printf("Before Current directory %s!\n",pathcd);
+   }
-    if(chdir(pathcd) != 0)
-     printf("Can't move to directory %s!\n",path);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-   if(getcwd(pathcd,MAXLINE) > 0)
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     printf("Current directory %s!\n",pathcd);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+ \n\
-   sprintf(plotcmd,"gnuplot");
+ <hr  size=\"2\" color=\"#EC5E5E\">\
- #ifndef UNIX
+  <ul><li><h4>Parameter files</h4>\n\
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
- #endif
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-   if(!stat(plotcmd,&info)){
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+  - Date and time at start: %s</ul>\n",\
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     }else
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-       strcpy(pplotcmd,plotcmd);
+           fileres,fileres,\
- #ifdef UNIX
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+   fflush(fichtm);
-     if(!stat(plotcmd,&info)){
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+   strcpy(pathr,path);
-     }else
+   strcat(pathr,optionfilefiname);
-       strcpy(pplotcmd,plotcmd);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
- #endif
-   }else
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-     strcpy(pplotcmd,plotcmd);
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-   if((outcmd=system(plotcmd)) != 0){
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-     printf("\n Problem with gnuplot\n");
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-   }
+           imx,agemin,agemax,jmin,jmax,jmean);
-   printf(" Wait...");
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   while (z[0] != 'q') {
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     /* chdir(path); */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     scanf("%s",z);
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
- /*     if (z[0] == 'c') system("./imach"); */
-     if (z[0] == 'e') {
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-       system(optionfilehtm);
+      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 if (z[0] == 'g') system(plotcmd);
-     else if (z[0] == 'q') exit(0);
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-   }
-   end:
+   if (mle==-3){
-   while (z[0] != 'q') {
+     ximort=matrix(1,NDIM,1,NDIM);
-     printf("\nType  q for exiting: ");
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     scanf("%s",z);
+     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);
+   }
+ }

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