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Diff for /imach/src/imach.c between versions 1.125 and 1.182

-version 1.125, 2006/04/04 15:20:31
+version 1.182, 2015/02/12 08:19:57
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
+   Revision 1.168  2014/12/22 15:17:42  brouard
+   Summary: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
    Revision 1.125  2006/04/04 15:20:31  lievre
    Errors in calculation of health expectancies. Age was not initialized.
    Forecasting file added.
    Revision 1.124  2006/03/22 17:13:53  lievre
    Parameters are printed with %lf instead of %f (more numbers after the comma).
    The log-likelihood is printed in the log file
    Revision 1.123  2006/03/20 10:52:43  brouard
    * imach.c (Module): <title> changed, corresponds to .htm file
    name. <head> headers where missing.
    * imach.c (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.122  2006/03/20 09:45:41  brouard
    (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.121  2006/03/16 17:45:01  lievre
    * imach.c (Module): Comments concerning covariates added
    * imach.c (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.120  2006/03/16 15:10:38  lievre
    (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.119  2006/03/15 17:42:26  brouard
    (Module): Bug if status = -2, the loglikelihood was
    computed as likelihood omitting the logarithm. Version O.98e
    Revision 1.118  2006/03/14 18:20:07  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.117  2006/03/14 17:16:22  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.116  2006/03/06 10:29:27  brouard
    (Module): Variance-covariance wrong links and
    varian-covariance of ej. is needed (Saito).
    Revision 1.115  2006/02/27 12:17:45  brouard
    (Module): One freematrix added in mlikeli! 0.98c
    Revision 1.114  2006/02/26 12:57:58  brouard
    (Module): Some improvements in processing parameter
    filename with strsep.
    Revision 1.113  2006/02/24 14:20:24  brouard
    (Module): Memory leaks checks with valgrind and:
    datafile was not closed, some imatrix were not freed and on matrix
    allocation too.
    Revision 1.112  2006/01/30 09:55:26  brouard
    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    Revision 1.111  2006/01/25 20:38:18  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    (Module): Comments can be added in data file. Missing date values
    can be a simple dot '.'.
    Revision 1.110  2006/01/25 00:51:50  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    Revision 1.109  2006/01/24 19:37:15  brouard
    (Module): Comments (lines starting with a #) are allowed in data.
    Revision 1.108  2006/01/19 18:05:42  lievre
    Gnuplot problem appeared...
    To be fixed
    Revision 1.107  2006/01/19 16:20:37  brouard
    Test existence of gnuplot in imach path
    Revision 1.106  2006/01/19 13:24:36  brouard
    Some cleaning and links added in html output
    Revision 1.105  2006/01/05 20:23:19  lievre
    *** empty log message ***
    Revision 1.104  2005/09/30 16:11:43  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    (Module): If the status is missing at the last wave but we know
    that the person is alive, then we can code his/her status as -2
    (instead of missing=-1 in earlier versions) and his/her
    contributions to the likelihood is 1 - Prob of dying from last
    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    the healthy state at last known wave). Version is 0.98
    Revision 1.103  2005/09/30 15:54:49  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    Revision 1.102  2004/09/15 17:31:30  brouard
    Add the possibility to read data file including tab characters.
    Revision 1.101  2004/09/15 10:38:38  brouard
    Fix on curr_time
    Revision 1.100  2004/07/12 18:29:06  brouard
    Add version for Mac OS X. Just define UNIX in Makefile
    Revision 1.99  2004/06/05 08:57:40  brouard
    *** empty log message ***
    Revision 1.98  2004/05/16 15:05:56  brouard
    New version 0.97 . First attempt to estimate force of mortality
    directly from the data i.e. without the need of knowing the health
    state at each age, but using a Gompertz model: log u =a + b*age .
    This is the basic analysis of mortality and should be done before any
    other analysis, in order to test if the mortality estimated from the
    cross-longitudinal survey is different from the mortality estimated
    from other sources like vital statistic data.
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
    the slope with 95% confident intervals.
    Current limitations:
    A) Even if you enter covariates, i.e. with the
    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    B) There is no computation of Life Expectancy nor Life Table.
    Revision 1.97  2004/02/20 13:25:42  lievre
    Version 0.96d. Population forecasting command line is (temporarily)
    suppressed.
    Revision 1.96  2003/07/15 15:38:55  brouard
    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs.
    Revision 1.95  2003/07/08 07:54:34  brouard
    * imach.c (Repository):
    (Repository): Using imachwizard code to output a more meaningful covariance
    matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
    Revision 1.93  2003/06/25 16:33:55  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    (Module): Version 0.96b
    Revision 1.92  2003/06/25 16:30:45  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    Revision 1.91  2003/06/25 15:30:29  brouard
    * imach.c (Repository): Duplicated warning errors corrected.
    (Repository): Elapsed time after each iteration is now output. It
    helps to forecast when convergence will be reached. Elapsed time
    is stamped in powell.  We created a new html file for the graphs
    concerning matrix of covariance. It has extension -cov.htm.
    Revision 1.90  2003/06/24 12:34:15  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.88  2003/06/23 17:54:56  brouard
    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    Revision 1.87  2003/06/18 12:26:01  brouard
    Version 0.96
    Revision 1.86  2003/06/17 20:04:08  brouard
    (Module): Change position of html and gnuplot routines and added
    routine fileappend.
    Revision 1.85  2003/06/17 13:12:43  brouard
    * imach.c (Repository): Check when date of death was earlier that
    current date of interview. It may happen when the death was just
    prior to the death. In this case, dh was negative and likelihood
    was wrong (infinity). We still send an "Error" but patch by
    assuming that the date of death was just one stepm after the
    interview.
    (Repository): Because some people have very long ID (first column)
    we changed int to long in num[] and we added a new lvector for
    memory allocation. But we also truncated to 8 characters (left
    truncation)
    (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
    Revision 1.82  2003/06/05 15:57:20  brouard
    Add log in  imach.c and  fullversion number is now printed.
  */
  /*
     Interpolated Markov Chain
    Short summary of the programme:
    This program computes Healthy Life Expectancies from
    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    first survey ("cross") where individuals from different ages are
    interviewed on their health status or degree of disability (in the
    case of a health survey which is our main interest) -2- at least a
    second wave of interviews ("longitudinal") which measure each change
    (if any) in individual health status.  Health expectancies are
    computed from the time spent in each health state according to a
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
    probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
    complex model than "constant and age", you should modify the program
    where the markup *Covariates have to be included here again* invites
    you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
    multinomial logistic model, is clear when the delay between waves is not
    identical for each individual. Also, if a individual missed an
    intermediate interview, the information is lost, but taken into
    account using an interpolation or extrapolation.
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
    states. This elementary transition (by month, quarter,
    semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
  /*
    main
    read parameterfile
    read datafile
    concatwav
    freqsummary
    if (mle >= 1)
      mlikeli
    print results files
    if mle==1
       computes hessian
    read end of parameter file: agemin, agemax, bage, fage, estepm
        begin-prev-date,...
    open gnuplot file
    open html file
-   period (stable) prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
-   forecasting if prevfcast==1 prevforecast call prevalence()
-   health expectancies
+   h Pij x                         | pij_nom  ficrestpij
-   Variance-covariance of DFLE
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
-   prevalence()
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
-    movingaverage()
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
-   varevsij()
-   if popbased==1 varevsij(,popbased)
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
-   total life expectancies
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
-   Variance of period (stable) prevalence
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
-  end
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- */
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
- #include <math.h>
+   prevalence()
- #include <stdio.h>
+    movingaverage()
- #include <stdlib.h>
+   varevsij()
- #include <string.h>
+   if popbased==1 varevsij(,popbased)
- #include <unistd.h>
+   total life expectancies
+   Variance of period (stable) prevalence
- #include <limits.h>
+  end
- #include <sys/types.h>
+ */
- #include <sys/stat.h>
- #include <errno.h>
+ #define POWELL /* Instead of NLOPT */
- extern int errno;
+ #define POWELLDIRECT /* Directest to decide new direction instead of Powell test */
- /* #include <sys/time.h> */
+ #include <math.h>
- #include <time.h>
+ #include <stdio.h>
- #include "timeval.h"
+ #include <stdlib.h>
+ #include <string.h>
- /* #include <libintl.h> */
- /* #define _(String) gettext (String) */
+ #ifdef _WIN32
+ #include <io.h>
- #define MAXLINE 256
+ #include <windows.h>
+ #include <tchar.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #else
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <unistd.h>
- #define FILENAMELENGTH 132
+ #endif
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #include <limits.h>
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <sys/types.h>
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #if defined(__GNUC__)
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
- #define NINTERVMAX 8
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #include <sys/stat.h>
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #include <errno.h>
- #define NCOVMAX 8 /* Maximum number of covariates */
+ /* extern int errno; */
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ /* #ifdef LINUX */
- #define AGESUP 130
+ /* #include <time.h> */
- #define AGEBASE 40
+ /* #include "timeval.h" */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ /* #else */
- #ifdef UNIX
+ /* #include <sys/time.h> */
- #define DIRSEPARATOR '/'
+ /* #endif */
- #define CHARSEPARATOR "/"
- #define ODIRSEPARATOR '\\'
+ #include <time.h>
- #else
- #define DIRSEPARATOR '\\'
+ #ifdef GSL
- #define CHARSEPARATOR "\\"
+ #include <gsl/gsl_errno.h>
- #define ODIRSEPARATOR '/'
+ #include <gsl/gsl_multimin.h>
  #endif
- /* $Id$ */
- /* $State$ */
+ #ifdef NLOPT
+ #include <nlopt.h>
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ typedef struct {
- char fullversion[]="$Revision$ $Date$";
+   double (* function)(double [] );
- char strstart[80];
+ } myfunc_data ;
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #endif
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ /* #include <libintl.h> */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ /* #define _(String) gettext (String) */
- int npar=NPARMAX;
- int nlstate=2; /* Number of live states */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- int ndeath=1; /* Number of dead states */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ #define GNUPLOTPROGRAM "gnuplot"
- int popbased=0;
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #define FILENAMELENGTH 132
- int *wav; /* Number of waves for this individuual 0 is possible */
- int maxwav; /* Maxim number of waves */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int mle, weightopt;
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define NINTERVMAX 8
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- double jmean; /* Mean space between 2 waves */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define MAXN 20000
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define YEARM 12. /**< Number of months per year */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define AGESUP 130
- FILE *ficlog, *ficrespow;
+ #define AGEBASE 40
- int globpr; /* Global variable for printing or not */
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- double fretone; /* Only one call to likelihood */
+ #ifdef _WIN32
- long ipmx; /* Number of contributions */
+ #define DIRSEPARATOR '\\'
- double sw; /* Sum of weights */
+ #define CHARSEPARATOR "\\"
- char filerespow[FILENAMELENGTH];
+ #define ODIRSEPARATOR '/'
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ #else
- FILE *ficresilk;
+ #define DIRSEPARATOR '/'
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ #define CHARSEPARATOR "/"
- FILE *ficresprobmorprev;
+ #define ODIRSEPARATOR '\\'
- FILE *fichtm, *fichtmcov; /* Html File */
+ #endif
- FILE *ficreseij;
- char filerese[FILENAMELENGTH];
+ /* $Id$ */
- FILE *ficresstdeij;
+ /* $State$ */
- char fileresstde[FILENAMELENGTH];
- FILE *ficrescveij;
+ char version[]="Imach version 0.98p, Février 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
- char filerescve[FILENAMELENGTH];
+ char fullversion[]="$Revision$ $Date$";
- FILE  *ficresvij;
+ char strstart[80];
- char fileresv[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- FILE  *ficresvpl;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char fileresvpl[FILENAMELENGTH];
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char title[MAXLINE];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char command[FILENAMELENGTH];
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- int  outcmd=0;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int cptcov=0; /* Working variable */
+ int npar=NPARMAX;
- char filelog[FILENAMELENGTH]; /* Log file */
+ int nlstate=2; /* Number of live states */
- char filerest[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
- char fileregp[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char popfile[FILENAMELENGTH];
+ int popbased=0;
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int *wav; /* Number of waves for this individuual 0 is possible */
+ int maxwav=0; /* Maxim number of waves */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- struct timezone tzp;
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- extern int gettimeofday();
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+                    to the likelihood and the sum of weights (done by funcone)*/
- long time_value;
+ int mle=1, weightopt=0;
- extern long time();
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- char strcurr[80], strfor[80];
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- char *endptr;
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- long lval;
+ int countcallfunc=0;  /* Count the number of calls to func */
- double dval;
+ double jmean=1; /* Mean space between 2 waves */
+ double **matprod2(); /* test */
- #define NR_END 1
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- #define FREE_ARG char*
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- #define FTOL 1.0e-10
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- #define NRANSI
+ FILE *ficlog, *ficrespow;
- #define ITMAX 200
+ int globpr=0; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
- #define TOL 2.0e-4
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- #define CGOLD 0.3819660
+ char filerespow[FILENAMELENGTH];
- #define ZEPS 1.0e-10
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ FILE *ficresilk;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define GOLD 1.618034
+ FILE *ficresprobmorprev;
- #define GLIMIT 100.0
+ FILE *fichtm, *fichtmcov; /* Html File */
- #define TINY 1.0e-20
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
- static double maxarg1,maxarg2;
+ FILE *ficresstdeij;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ char fileresstde[FILENAMELENGTH];
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ FILE  *ficresvij;
- #define rint(a) floor(a+0.5)
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
- static double sqrarg;
+ char fileresvpl[FILENAMELENGTH];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ char title[MAXLINE];
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- int imx;
+ char command[FILENAMELENGTH];
- int stepm=1;
+ int  outcmd=0;
- /* Stepm, step in month: minimum step interpolation*/
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- int estepm;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
- int m,nb;
+ char fileregp[FILENAMELENGTH];
- long *num;
+ char popfile[FILENAMELENGTH];
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- double **pmmij, ***probs;
- double *ageexmed,*agecens;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- double dateintmean=0;
+ /* struct timezone tzp; */
+ /* extern int gettimeofday(); */
- double *weight;
+ struct tm tml, *gmtime(), *localtime();
- int **s; /* Status */
- double *agedc, **covar, idx;
+ extern time_t time();
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
- double *lsurv, *lpop, *tpop;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ struct tm tm;
- double ftolhess; /* Tolerance for computing hessian */
+ char strcurr[80], strfor[80];
- /**************** split *************************/
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ char *endptr;
- {
+ long lval;
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ double dval;
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ #define NR_END 1
-   char  *ss;                            /* pointer */
+ #define FREE_ARG char*
-   int   l1, l2;                         /* length counters */
+ #define FTOL 1.0e-10
-   l1 = strlen(path );                   /* length of path */
+ #define NRANSI
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define ITMAX 200
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ #define TOL 2.0e-4
-     strcpy( name, path );               /* we got the fullname name because no directory */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ #define CGOLD 0.3819660
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define ZEPS 1.0e-10
-     /* get current working directory */
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-     /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define GOLD 1.618034
-       return( GLOCK_ERROR_GETCWD );
+ #define GLIMIT 100.0
-     }
+ #define TINY 1.0e-20
-     /* got dirc from getcwd*/
-     printf(" DIRC = %s \n",dirc);
+ static double maxarg1,maxarg2;
-   } else {                              /* strip direcotry from path */
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     ss++;                               /* after this, the filename */
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     l2 = strlen( ss );                  /* length of filename */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     strcpy( name, ss );         /* save file name */
+ #define rint(a) floor(a+0.5)
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     dirc[l1-l2] = 0;                    /* add zero */
+ /* #define mytinydouble 1.0e-16 */
-     printf(" DIRC2 = %s \n",dirc);
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-   }
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-   /* We add a separator at the end of dirc if not exists */
+ /* static double dsqrarg; */
-   l1 = strlen( dirc );                  /* length of directory */
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ static double sqrarg;
-     dirc[l1] =  DIRSEPARATOR;
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-     dirc[l1+1] = 0;
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     printf(" DIRC3 = %s \n",dirc);
+ int agegomp= AGEGOMP;
-   }
-   ss = strrchr( name, '.' );            /* find last / */
+ int imx;
-   if (ss >0){
+ int stepm=1;
-     ss++;
+ /* Stepm, step in month: minimum step interpolation*/
-     strcpy(ext,ss);                     /* save extension */
-     l1= strlen( name);
+ int estepm;
-     l2= strlen(ss)+1;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     strncpy( finame, name, l1-l2);
-     finame[l1-l2]= 0;
+ int m,nb;
-   }
+ long *num;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-   return( 0 );                          /* we're done */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- }
+ double **pmmij, ***probs;
+ double *ageexmed,*agecens;
+ double dateintmean=0;
- /******************************************/
+ double *weight;
- void replace_back_to_slash(char *s, char*t)
+ int **s; /* Status */
- {
+ double *agedc;
-   int i;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   int lg=0;
+                   * covar=matrix(0,NCOVMAX,1,n);
-   i=0;
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   lg=strlen(t);
+ double  idx;
-   for(i=0; i<= lg; i++) {
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-     (s[i] = t[i]);
+ int *Ndum; /** Freq of modality (tricode */
-     if (t[i]== '\\') s[i]='/';
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   }
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
- }
+ double *lsurv, *lpop, *tpop;
- int nbocc(char *s, char occ)
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- {
+ double ftolhess; /**< Tolerance for computing hessian */
-   int i,j=0;
-   int lg=20;
+ /**************** split *************************/
-   i=0;
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   lg=strlen(s);
+ {
-   for(i=0; i<= lg; i++) {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   if  (s[i] == occ ) j++;
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   }
+   */
-   return j;
+   char  *ss;                            /* pointer */
- }
+   int   l1, l2;                         /* length counters */
- void cutv(char *u,char *v, char*t, char occ)
+   l1 = strlen(path );                   /* length of path */
- {
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-      gives u="abcedf" and v="ghi2j" */
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   int i,lg,j,p=0;
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   i=0;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   for(j=0; j<=strlen(t)-1; j++) {
+     /* get current working directory */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   }
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+       return( GLOCK_ERROR_GETCWD );
-   lg=strlen(t);
+     }
-   for(j=0; j<p; j++) {
+     /* got dirc from getcwd*/
-     (u[j] = t[j]);
+     printf(" DIRC = %s \n",dirc);
-   }
+   } else {                              /* strip direcotry from path */
-      u[p]='\0';
+     ss++;                               /* after this, the filename */
+     l2 = strlen( ss );                  /* length of filename */
-    for(j=0; j<= lg; j++) {
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     strcpy( name, ss );         /* save file name */
-   }
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
- }
+     dirc[l1-l2] = 0;                    /* add zero */
+     printf(" DIRC2 = %s \n",dirc);
- /********************** nrerror ********************/
+   }
+   /* We add a separator at the end of dirc if not exists */
- void nrerror(char error_text[])
+   l1 = strlen( dirc );                  /* length of directory */
- {
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   fprintf(stderr,"ERREUR ...\n");
+     dirc[l1] =  DIRSEPARATOR;
-   fprintf(stderr,"%s\n",error_text);
+     dirc[l1+1] = 0;
-   exit(EXIT_FAILURE);
+     printf(" DIRC3 = %s \n",dirc);
- }
+   }
- /*********************** vector *******************/
+   ss = strrchr( name, '.' );            /* find last / */
- double *vector(int nl, int nh)
+   if (ss >0){
- {
+     ss++;
-   double *v;
+     strcpy(ext,ss);                     /* save extension */
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     l1= strlen( name);
-   if (!v) nrerror("allocation failure in vector");
+     l2= strlen(ss)+1;
-   return v-nl+NR_END;
+     strncpy( finame, name, l1-l2);
- }
+     finame[l1-l2]= 0;
+   }
- /************************ free vector ******************/
- void free_vector(double*v, int nl, int nh)
+   return( 0 );                          /* we're done */
- {
+ }
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ /******************************************/
- /************************ivector *******************************/
- int *ivector(long nl,long nh)
+ void replace_back_to_slash(char *s, char*t)
  {
-   int *v;
+   int i;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   int lg=0;
-   if (!v) nrerror("allocation failure in ivector");
+   i=0;
-   return v-nl+NR_END;
+   lg=strlen(t);
- }
+   for(i=0; i<= lg; i++) {
+     (s[i] = t[i]);
- /******************free ivector **************************/
+     if (t[i]== '\\') s[i]='/';
- void free_ivector(int *v, long nl, long nh)
+   }
- {
+ }
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ char *trimbb(char *out, char *in)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
- /************************lvector *******************************/
+   char *s;
- long *lvector(long nl,long nh)
+   s=out;
- {
+   while (*in != '\0'){
-   long *v;
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+       in++;
-   if (!v) nrerror("allocation failure in ivector");
+     }
-   return v-nl+NR_END;
+     *out++ = *in++;
- }
+   }
+   *out='\0';
- /******************free lvector **************************/
+   return s;
- void free_lvector(long *v, long nl, long nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- }
+ {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
- /******************* imatrix *******************************/
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+      gives blocc="abcdef2ghi" and alocc="j".
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- {
+   */
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   char *s, *t;
-   int **m;
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
-   /* allocate pointers to rows */
+     *alocc++ = *in++;
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   }
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   if( *in == occ){
-   m += NR_END;
+     *(alocc)='\0';
-   m -= nrl;
+     s=++in;
+   }
-   /* allocate rows and set pointers to them */
+   if (s == t) {/* occ not found */
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+     *(alocc-(in-s))='\0';
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     in=s;
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   while ( *in != '\0'){
+     *blocc++ = *in++;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   }
-   /* return pointer to array of pointers to rows */
+   *blocc='\0';
-   return m;
+   return t;
  }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
- /****************** free_imatrix *************************/
+ {
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-       int **m;
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-       long nch,ncl,nrh,nrl;
+      gives blocc="abcdef2ghi" and alocc="j".
-      /* free an int matrix allocated by imatrix() */
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
- {
+   */
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   char *s, *t;
-   free((FREE_ARG) (m+nrl-NR_END));
+   t=in;s=in;
- }
+   while (*in != '\0'){
+     while( *in == occ){
- /******************* matrix *******************************/
+       *blocc++ = *in++;
- double **matrix(long nrl, long nrh, long ncl, long nch)
+       s=in;
- {
+     }
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+     *blocc++ = *in++;
-   double **m;
+   }
+   if (s == t) /* occ not found */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+     *(blocc-(in-s))='\0';
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   else
-   m += NR_END;
+     *(blocc-(in-s)-1)='\0';
-   m -= nrl;
+   in=s;
+   while ( *in != '\0'){
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     *alocc++ = *in++;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   }
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+   *alocc='\0';
+   return s;
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ }
-   return m;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ int nbocc(char *s, char occ)
-    */
+ {
- }
+   int i,j=0;
+   int lg=20;
- /*************************free matrix ************************/
+   i=0;
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   lg=strlen(s);
- {
+   for(i=0; i<= lg; i++) {
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   if  (s[i] == occ ) j++;
-   free((FREE_ARG)(m+nrl-NR_END));
+   }
- }
+   return j;
+ }
- /******************* ma3x *******************************/
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /* void cutv(char *u,char *v, char*t, char occ) */
- {
+ /* { */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   double ***m;
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*   int i,lg,j,p=0; */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*   i=0; */
-   m += NR_END;
+ /*   lg=strlen(t); */
-   m -= nrl;
+ /*   for(j=0; j<=lg-1; j++) { */
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   } */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+ /*   for(j=0; j<p; j++) { */
-   m[nrl] -= ncl;
+ /*     (u[j] = t[j]); */
+ /*   } */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*      u[p]='\0'; */
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ /*    for(j=0; j<= lg; j++) { */
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   m[nrl][ncl] += NR_END;
+ /*   } */
-   m[nrl][ncl] -= nll;
+ /* } */
-   for (j=ncl+1; j<=nch; j++)
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ #ifdef _WIN32
+ char * strsep(char **pp, const char *delim)
-   for (i=nrl+1; i<=nrh; i++) {
+ {
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   char *p, *q;
-     for (j=ncl+1; j<=nch; j++)
-       m[i][j]=m[i][j-1]+nlay;
+   if ((p = *pp) == NULL)
-   }
+     return 0;
-   return m;
+   if ((q = strpbrk (p, delim)) != NULL)
-   /*  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)
+     *pp = q + 1;
-   */
+     *q = '\0';
- }
+   }
+   else
- /*************************free ma3x ************************/
+     *pp = 0;
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   return p;
- {
+ }
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ #endif
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+ /********************** nrerror ********************/
- }
+ void nrerror(char error_text[])
- /*************** function subdirf ***********/
+ {
- char *subdirf(char fileres[])
+   fprintf(stderr,"ERREUR ...\n");
- {
+   fprintf(stderr,"%s\n",error_text);
-   /* Caution optionfilefiname is hidden */
+   exit(EXIT_FAILURE);
-   strcpy(tmpout,optionfilefiname);
+ }
-   strcat(tmpout,"/"); /* Add to the right */
+ /*********************** vector *******************/
-   strcat(tmpout,fileres);
+ double *vector(int nl, int nh)
-   return tmpout;
+ {
- }
+   double *v;
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
- /*************** function subdirf2 ***********/
+   if (!v) nrerror("allocation failure in vector");
- char *subdirf2(char fileres[], char *preop)
+   return v-nl+NR_END;
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /************************ free vector ******************/
-   strcpy(tmpout,optionfilefiname);
+ void free_vector(double*v, int nl, int nh)
-   strcat(tmpout,"/");
+ {
-   strcat(tmpout,preop);
+   free((FREE_ARG)(v+nl-NR_END));
-   strcat(tmpout,fileres);
+ }
-   return tmpout;
- }
+ /************************ivector *******************************/
+ int *ivector(long nl,long nh)
- /*************** function subdirf3 ***********/
+ {
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   int *v;
- {
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   if (!v) nrerror("allocation failure in ivector");
-   /* Caution optionfilefiname is hidden */
+   return v-nl+NR_END;
-   strcpy(tmpout,optionfilefiname);
+ }
-   strcat(tmpout,"/");
-   strcat(tmpout,preop);
+ /******************free ivector **************************/
-   strcat(tmpout,preop2);
+ void free_ivector(int *v, long nl, long nh)
-   strcat(tmpout,fileres);
+ {
-   return tmpout;
+   free((FREE_ARG)(v+nl-NR_END));
  }
- /***************** f1dim *************************/
+ /************************lvector *******************************/
- extern int ncom;
+ long *lvector(long nl,long nh)
- extern double *pcom,*xicom;
+ {
- extern double (*nrfunc)(double []);
+   long *v;
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
- double f1dim(double x)
+   if (!v) nrerror("allocation failure in ivector");
- {
+   return v-nl+NR_END;
-   int j;
+ }
-   double f;
-   double *xt;
+ /******************free lvector **************************/
+ void free_lvector(long *v, long nl, long nh)
-   xt=vector(1,ncom);
+ {
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   free((FREE_ARG)(v+nl-NR_END));
-   f=(*nrfunc)(xt);
+ }
-   free_vector(xt,1,ncom);
-   return f;
+ /******************* imatrix *******************************/
- }
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
- /*****************brent *************************/
+ {
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
- {
+   int **m;
-   int iter;
-   double a,b,d,etemp;
+   /* allocate pointers to rows */
-   double fu,fv,fw,fx;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   double ftemp;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   m += NR_END;
-   double e=0.0;
+   m -= nrl;
-   a=(ax < cx ? ax : cx);
-   b=(ax > cx ? ax : cx);
+   /* allocate rows and set pointers to them */
-   x=w=v=bx;
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   fw=fv=fx=(*f)(x);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   for (iter=1;iter<=ITMAX;iter++) {
+   m[nrl] += NR_END;
-     xm=0.5*(a+b);
+   m[nrl] -= ncl;
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-     printf(".");fflush(stdout);
-     fprintf(ficlog,".");fflush(ficlog);
+   /* return pointer to array of pointers to rows */
- #ifdef DEBUG
+   return m;
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ }
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+ /****************** free_imatrix *************************/
- #endif
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+       int **m;
-       *xmin=x;
+       long nch,ncl,nrh,nrl;
-       return fx;
+      /* free an int matrix allocated by imatrix() */
-     }
+ {
-     ftemp=fu;
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     if (fabs(e) > tol1) {
+   free((FREE_ARG) (m+nrl-NR_END));
-       r=(x-w)*(fx-fv);
+ }
-       q=(x-v)*(fx-fw);
-       p=(x-v)*q-(x-w)*r;
+ /******************* matrix *******************************/
-       q=2.0*(q-r);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       if (q > 0.0) p = -p;
+ {
-       q=fabs(q);
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-       etemp=e;
+   double **m;
-       e=d;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       else {
+   m += NR_END;
-         d=p/q;
+   m -= nrl;
-         u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-           d=SIGN(tol1,xm-x);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       }
+   m[nrl] += NR_END;
-     } else {
+   m[nrl] -= ncl;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   return m;
-     fu=(*f)(u);
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-     if (fu <= fx) {
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-       if (u >= x) a=x; else b=x;
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-       SHFT(v,w,x,u)
+    */
-         SHFT(fv,fw,fx,fu)
+ }
-         } else {
-           if (u < x) a=u; else b=u;
+ /*************************free matrix ************************/
-           if (fu <= fw || w == x) {
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-             v=w;
+ {
-             w=u;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-             fv=fw;
+   free((FREE_ARG)(m+nrl-NR_END));
-             fw=fu;
+ }
-           } else if (fu <= fv || v == x || v == w) {
-             v=u;
+ /******************* ma3x *******************************/
-             fv=fu;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-           }
+ {
-         }
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-   }
+   double ***m;
-   nrerror("Too many iterations in brent");
-   *xmin=x;
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   return fx;
+   if (!m) nrerror("allocation failure 1 in matrix()");
- }
+   m += NR_END;
+   m -= nrl;
- /****************** mnbrak ***********************/
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-             double (*func)(double))
+   m[nrl] += NR_END;
- {
+   m[nrl] -= ncl;
-   double ulim,u,r,q, dum;
-   double fu;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   *fa=(*func)(*ax);
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   *fb=(*func)(*bx);
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   if (*fb > *fa) {
+   m[nrl][ncl] += NR_END;
-     SHFT(dum,*ax,*bx,dum)
+   m[nrl][ncl] -= nll;
-       SHFT(dum,*fb,*fa,dum)
+   for (j=ncl+1; j<=nch; j++)
-       }
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   *cx=(*bx)+GOLD*(*bx-*ax);
-   *fc=(*func)(*cx);
+   for (i=nrl+1; i<=nrh; i++) {
-   while (*fb > *fc) {
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-     r=(*bx-*ax)*(*fb-*fc);
+     for (j=ncl+1; j<=nch; j++)
-     q=(*bx-*cx)*(*fb-*fa);
+       m[i][j]=m[i][j-1]+nlay;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   }
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   return m;
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-     if ((*bx-u)*(u-*cx) > 0.0) {
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-       fu=(*func)(u);
+   */
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ }
-       fu=(*func)(u);
-       if (fu < *fc) {
+ /*************************free ma3x ************************/
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-           SHFT(*fb,*fc,fu,(*func)(u))
+ {
-           }
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-       u=ulim;
+   free((FREE_ARG)(m+nrl-NR_END));
-       fu=(*func)(u);
+ }
-     } else {
-       u=(*cx)+GOLD*(*cx-*bx);
+ /*************** function subdirf ***********/
-       fu=(*func)(u);
+ char *subdirf(char fileres[])
-     }
+ {
-     SHFT(*ax,*bx,*cx,u)
+   /* Caution optionfilefiname is hidden */
-       SHFT(*fa,*fb,*fc,fu)
+   strcpy(tmpout,optionfilefiname);
-       }
+   strcat(tmpout,"/"); /* Add to the right */
- }
+   strcat(tmpout,fileres);
+   return tmpout;
- /*************** linmin ************************/
+ }
- int ncom;
+ /*************** function subdirf2 ***********/
- double *pcom,*xicom;
+ char *subdirf2(char fileres[], char *preop)
- double (*nrfunc)(double []);
+ {
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   /* Caution optionfilefiname is hidden */
- {
+   strcpy(tmpout,optionfilefiname);
-   double brent(double ax, double bx, double cx,
+   strcat(tmpout,"/");
-                double (*f)(double), double tol, double *xmin);
+   strcat(tmpout,preop);
-   double f1dim(double x);
+   strcat(tmpout,fileres);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   return tmpout;
-               double *fc, double (*func)(double));
+ }
-   int j;
-   double xx,xmin,bx,ax;
+ /*************** function subdirf3 ***********/
-   double fx,fb,fa;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
-   ncom=n;
-   pcom=vector(1,n);
+   /* Caution optionfilefiname is hidden */
-   xicom=vector(1,n);
+   strcpy(tmpout,optionfilefiname);
-   nrfunc=func;
+   strcat(tmpout,"/");
-   for (j=1;j<=n;j++) {
+   strcat(tmpout,preop);
-     pcom[j]=p[j];
+   strcat(tmpout,preop2);
-     xicom[j]=xi[j];
+   strcat(tmpout,fileres);
-   }
+   return tmpout;
-   ax=0.0;
+ }
-   xx=1.0;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ {
- #ifdef DEBUG
+   long sec_left, days, hours, minutes;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   days = (time_sec) / (60*60*24);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   sec_left = (time_sec) % (60*60*24);
- #endif
+   hours = (sec_left) / (60*60) ;
-   for (j=1;j<=n;j++) {
+   sec_left = (sec_left) %(60*60);
-     xi[j] *= xmin;
+   minutes = (sec_left) /60;
-     p[j] += xi[j];
+   sec_left = (sec_left) % (60);
-   }
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-   free_vector(xicom,1,n);
+   return ascdiff;
-   free_vector(pcom,1,n);
+ }
- }
+ /***************** f1dim *************************/
- char *asc_diff_time(long time_sec, char ascdiff[])
+ extern int ncom;
- {
+ extern double *pcom,*xicom;
-   long sec_left, days, hours, minutes;
+ extern double (*nrfunc)(double []);
-   days = (time_sec) / (60*60*24);
-   sec_left = (time_sec) % (60*60*24);
+ double f1dim(double x)
-   hours = (sec_left) / (60*60) ;
+ {
-   sec_left = (sec_left) %(60*60);
+   int j;
-   minutes = (sec_left) /60;
+   double f;
-   sec_left = (sec_left) % (60);
+   double *xt;
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
-   return ascdiff;
+   xt=vector(1,ncom);
- }
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   f=(*nrfunc)(xt);
- /*************** powell ************************/
+   free_vector(xt,1,ncom);
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   return f;
-             double (*func)(double []))
+ }
- {
-   void linmin(double p[], double xi[], int n, double *fret,
+ /*****************brent *************************/
-               double (*func)(double []));
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-   int i,ibig,j;
+ {
-   double del,t,*pt,*ptt,*xit;
+   int iter;
-   double fp,fptt;
+   double a,b,d,etemp;
-   double *xits;
+   double fu=0,fv,fw,fx;
-   int niterf, itmp;
+   double ftemp=0.;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   pt=vector(1,n);
+   double e=0.0;
-   ptt=vector(1,n);
-   xit=vector(1,n);
+   a=(ax < cx ? ax : cx);
-   xits=vector(1,n);
+   b=(ax > cx ? ax : cx);
-   *fret=(*func)(p);
+   x=w=v=bx;
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   fw=fv=fx=(*f)(x);
-   for (*iter=1;;++(*iter)) {
+   for (iter=1;iter<=ITMAX;iter++) {
-     fp=(*fret);
+     xm=0.5*(a+b);
-     ibig=0;
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-     del=0.0;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     last_time=curr_time;
+     printf(".");fflush(stdout);
-     (void) gettimeofday(&curr_time,&tzp);
+     fprintf(ficlog,".");fflush(ficlog);
-     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);
+ #ifdef DEBUGBRENT
-     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);
+     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-    for (i=1;i<=n;i++) {
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-       printf(" %d %.12f",i, p[i]);
+ #endif
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       fprintf(ficrespow," %.12lf", p[i]);
+       *xmin=x;
-     }
+       return fx;
-     printf("\n");
+     }
-     fprintf(ficlog,"\n");
+     ftemp=fu;
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if (fabs(e) > tol1) {
-     if(*iter <=3){
+       r=(x-w)*(fx-fv);
-       tm = *localtime(&curr_time.tv_sec);
+       q=(x-v)*(fx-fw);
-       strcpy(strcurr,asctime(&tm));
+       p=(x-v)*q-(x-w)*r;
- /*       asctime_r(&tm,strcurr); */
+       q=2.0*(q-r);
-       forecast_time=curr_time;
+       if (q > 0.0) p = -p;
-       itmp = strlen(strcurr);
+       q=fabs(q);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+       etemp=e;
-         strcurr[itmp-1]='\0';
+       e=d;
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       for(niterf=10;niterf<=30;niterf+=10){
+       else {
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         d=p/q;
-         tmf = *localtime(&forecast_time.tv_sec);
+         u=x+d;
- /*      asctime_r(&tmf,strfor); */
+         if (u-a < tol2 || b-u < tol2)
-         strcpy(strfor,asctime(&tmf));
+           d=SIGN(tol1,xm-x);
-         itmp = strlen(strfor);
+       }
-         if(strfor[itmp-1]=='\n')
+     } else {
-         strfor[itmp-1]='\0';
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     }
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-       }
+     fu=(*f)(u);
-     }
+     if (fu <= fx) {
-     for (i=1;i<=n;i++) {
+       if (u >= x) a=x; else b=x;
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+       SHFT(v,w,x,u)
-       fptt=(*fret);
+         SHFT(fv,fw,fx,fu)
- #ifdef DEBUG
+         } else {
-       printf("fret=%lf \n",*fret);
+           if (u < x) a=u; else b=u;
-       fprintf(ficlog,"fret=%lf \n",*fret);
+           if (fu <= fw || w == x) {
- #endif
+             v=w;
-       printf("%d",i);fflush(stdout);
+             w=u;
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+             fv=fw;
-       linmin(p,xit,n,fret,func);
+             fw=fu;
-       if (fabs(fptt-(*fret)) > del) {
+           } else if (fu <= fv || v == x || v == w) {
-         del=fabs(fptt-(*fret));
+             v=u;
-         ibig=i;
+             fv=fu;
-       }
+           }
- #ifdef DEBUG
+         }
-       printf("%d %.12e",i,(*fret));
+   }
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   nrerror("Too many iterations in brent");
-       for (j=1;j<=n;j++) {
+   *xmin=x;
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   return fx;
-         printf(" x(%d)=%.12e",j,xit[j]);
+ }
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       }
+ /****************** mnbrak ***********************/
-       for(j=1;j<=n;j++) {
-         printf(" p=%.12e",p[j]);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         fprintf(ficlog," p=%.12e",p[j]);
+             double (*func)(double))
-       }
+ {
-       printf("\n");
+   double ulim,u,r,q, dum;
-       fprintf(ficlog,"\n");
+   double fu;
- #endif
-     }
+   *fa=(*func)(*ax);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   *fb=(*func)(*bx);
- #ifdef DEBUG
+   if (*fb > *fa) {
-       int k[2],l;
+     SHFT(dum,*ax,*bx,dum)
-       k[0]=1;
+       SHFT(dum,*fb,*fa,dum)
-       k[1]=-1;
+       }
-       printf("Max: %.12e",(*func)(p));
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   *fc=(*func)(*cx);
-       for (j=1;j<=n;j++) {
+   while (*fb > *fc) { /* Declining fa, fb, fc */
-         printf(" %.12e",p[j]);
+     r=(*bx-*ax)*(*fb-*fc);
-         fprintf(ficlog," %.12e",p[j]);
+     q=(*bx-*cx)*(*fb-*fa);
-       }
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       printf("\n");
+       (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,"\n");
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-       for(l=0;l<=1;l++) {
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
-         for (j=1;j<=n;j++) {
+       fu=(*func)(u);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+ #ifdef DEBUG
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       /* f(x)=A(x-u)**2+f(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]);
+       double A, fparabu;
-         }
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-       }
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
  #endif
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+       fu=(*func)(u);
-       free_vector(xit,1,n);
+       if (fu < *fc) {
-       free_vector(xits,1,n);
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-       free_vector(ptt,1,n);
+           SHFT(*fb,*fc,fu,(*func)(u))
-       free_vector(pt,1,n);
+           }
-       return;
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-     }
+       u=ulim;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+       fu=(*func)(u);
-     for (j=1;j<=n;j++) {
+     } else {
-       ptt[j]=2.0*p[j]-pt[j];
+       u=(*cx)+GOLD*(*cx-*bx);
-       xit[j]=p[j]-pt[j];
+       fu=(*func)(u);
-       pt[j]=p[j];
+     }
-     }
+     SHFT(*ax,*bx,*cx,u)
-     fptt=(*func)(ptt);
+       SHFT(*fa,*fb,*fc,fu)
-     if (fptt < fp) {
+       }
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ }
-       if (t < 0.0) {
-         linmin(p,xit,n,fret,func);
+ /*************** linmin ************************/
-         for (j=1;j<=n;j++) {
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-           xi[j][ibig]=xi[j][n];
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-           xi[j][n]=xit[j];
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-         }
+ the value of func at the returned location p . This is actually all accomplished by calling the
- #ifdef DEBUG
+ routines mnbrak and brent .*/
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ int ncom;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ double *pcom,*xicom;
-         for(j=1;j<=n;j++){
+ double (*nrfunc)(double []);
-           printf(" %.12e",xit[j]);
-           fprintf(ficlog," %.12e",xit[j]);
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-         }
+ {
-         printf("\n");
+   double brent(double ax, double bx, double cx,
-         fprintf(ficlog,"\n");
+                double (*f)(double), double tol, double *xmin);
- #endif
+   double f1dim(double x);
-       }
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-     }
+               double *fc, double (*func)(double));
-   }
+   int j;
- }
+   double xx,xmin,bx,ax;
+   double fx,fb,fa;
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   ncom=n;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   pcom=vector(1,n);
- {
+   xicom=vector(1,n);
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   nrfunc=func;
-      matrix by transitions matrix until convergence is reached */
+   for (j=1;j<=n;j++) {
+     pcom[j]=p[j];
-   int i, ii,j,k;
+     xicom[j]=xi[j];
-   double min, max, maxmin, maxmax,sumnew=0.;
+   }
-   double **matprod2();
+   ax=0.0;
-   double **out, cov[NCOVMAX], **pmij();
+   xx=1.0;
-   double **newm;
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
+ #ifdef DEBUG
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     for (j=1;j<=nlstate+ndeath;j++){
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ #endif
-     }
+   for (j=1;j<=n;j++) {
+     xi[j] *= xmin;
-    cov[1]=1.;
+     p[j] += xi[j];
+   }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   free_vector(xicom,1,n);
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+   free_vector(pcom,1,n);
-     newm=savm;
+ }
-     /* Covariates have to be included here again */
-      cov[2]=agefin;
+ /*************** powell ************************/
-       for (k=1; k<=cptcovn;k++) {
+ /*
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ Minimization of a function func of n variables. Input consists of an initial starting point
-         /*      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]]);*/
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-       }
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-       for (k=1; k<=cptcovprod;k++)
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
+  */
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+ void powell(double p[], double **xi, int n, double ftol, int *iter, 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]);*/
+ {
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   void linmin(double p[], double xi[], int n, double *fret,
+               double (*func)(double []));
-     savm=oldm;
+   int i,ibig,j;
-     oldm=newm;
+   double del,t,*pt,*ptt,*xit;
-     maxmax=0.;
+   double directest;
-     for(j=1;j<=nlstate;j++){
+   double fp,fptt;
-       min=1.;
+   double *xits;
-       max=0.;
+   int niterf, itmp;
-       for(i=1; i<=nlstate; i++) {
-         sumnew=0;
+   pt=vector(1,n);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+   ptt=vector(1,n);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+   xit=vector(1,n);
-         max=FMAX(max,prlim[i][j]);
+   xits=vector(1,n);
-         min=FMIN(min,prlim[i][j]);
+   *fret=(*func)(p);
-       }
+   for (j=1;j<=n;j++) pt[j]=p[j];
-       maxmin=max-min;
+     rcurr_time = time(NULL);
-       maxmax=FMAX(maxmax,maxmin);
+   for (*iter=1;;++(*iter)) {
-     }
+     fp=(*fret);
-     if(maxmax < ftolpl){
+     ibig=0;
-       return prlim;
+     del=0.0;
-     }
+     rlast_time=rcurr_time;
-   }
+     /* (void) gettimeofday(&curr_time,&tzp); */
- }
+     rcurr_time = time(NULL);
+     curr_time = *localtime(&rcurr_time);
- /*************** transition probabilities ***************/
+     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);
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
- {
+    for (i=1;i<=n;i++) {
-   double s1, s2;
+       printf(" %d %.12f",i, p[i]);
-   /*double t34;*/
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-   int i,j,j1, nc, ii, jj;
+       fprintf(ficrespow," %.12lf", p[i]);
+     }
-     for(i=1; i<= nlstate; i++){
+     printf("\n");
-       for(j=1; j<i;j++){
+     fprintf(ficlog,"\n");
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+     if(*iter <=3){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       tml = *localtime(&rcurr_time);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+       strcpy(strcurr,asctime(&tml));
-         }
+       rforecast_time=rcurr_time;
-         ps[i][j]=s2;
+       itmp = strlen(strcurr);
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       }
+         strcurr[itmp-1]='\0';
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       for(niterf=10;niterf<=30;niterf+=10){
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-         }
+         forecast_time = *localtime(&rforecast_time);
-         ps[i][j]=s2;
+         strcpy(strfor,asctime(&forecast_time));
-       }
+         itmp = strlen(strfor);
-     }
+         if(strfor[itmp-1]=='\n')
-     /*ps[3][2]=1;*/
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-     for(i=1; i<= nlstate; i++){
+         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);
-       s1=0;
+       }
-       for(j=1; j<i; j++)
+     }
-         s1+=exp(ps[i][j]);
+     for (i=1;i<=n;i++) {
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-         s1+=exp(ps[i][j]);
+       fptt=(*fret);
-       ps[i][i]=1./(s1+1.);
+ #ifdef DEBUG
-       for(j=1; j<i; j++)
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ #endif
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       printf("%d",i);fflush(stdout);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     } /* end i */
+       linmin(p,xit,n,fret,func);
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+                                        because that direction will be replaced unless the gain del is small
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+                                       in comparison with the 'probable' gain, mu^2, with the last average direction.
-         ps[ii][jj]=0;
+                                       Unless the n directions are conjugate some gain in the determinant may be obtained
-         ps[ii][ii]=1;
+                                       with the new direction.
-       }
+                                       */
-     }
+         del=fabs(fptt-(*fret));
+         ibig=i;
+       }
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+ #ifdef DEBUG
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       printf("%d %.12e",i,(*fret));
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       fprintf(ficlog,"%d %.12e",i,(*fret));
- /*       } */
+       for (j=1;j<=n;j++) {
- /*       printf("\n "); */
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
- /*        } */
+         printf(" x(%d)=%.12e",j,xit[j]);
- /*        printf("\n ");printf("%lf ",cov[2]); */
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-        /*
+       }
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       for(j=1;j<=n;j++) {
-       goto end;*/
+         printf(" p(%d)=%.12e",j,p[j]);
-     return ps;
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
- }
+       }
+       printf("\n");
- /**************** Product of 2 matrices ******************/
+       fprintf(ficlog,"\n");
+ #endif
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+     } /* end i */
- {
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ #ifdef DEBUG
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+       int k[2],l;
-   /* in, b, out are matrice of pointers which should have been initialized
+       k[0]=1;
-      before: only the contents of out is modified. The function returns
+       k[1]=-1;
-      a pointer to pointers identical to out */
+       printf("Max: %.12e",(*func)(p));
-   long i, j, k;
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-   for(i=nrl; i<= nrh; i++)
+       for (j=1;j<=n;j++) {
-     for(k=ncolol; k<=ncoloh; k++)
+         printf(" %.12e",p[j]);
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+         fprintf(ficlog," %.12e",p[j]);
-         out[i][k] +=in[i][j]*b[j][k];
+       }
+       printf("\n");
-   return out;
+       fprintf(ficlog,"\n");
- }
+       for(l=0;l<=1;l++) {
+         for (j=1;j<=n;j++) {
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
- /************* Higher Matrix Product ***************/
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+         }
- {
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   /* Computes the transition matrix starting at age 'age' over
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-      'nhstepm*hstepm*stepm' months (i.e. until
+       }
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+ #endif
-      nhstepm*hstepm matrices.
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-      (typically every 2 years instead of every month which is too big
+       free_vector(xit,1,n);
-      for the memory).
+       free_vector(xits,1,n);
-      Model is determined by parameters x and covariates have to be
+       free_vector(ptt,1,n);
-      included manually here.
+       free_vector(pt,1,n);
+       return;
-      */
+     }
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-   int i, j, d, h, k;
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
-   double **out, cov[NCOVMAX];
+       ptt[j]=2.0*p[j]-pt[j];
-   double **newm;
+       xit[j]=p[j]-pt[j];
+       pt[j]=p[j];
-   /* Hstepm could be zero and should return the unit matrix */
+     }
-   for (i=1;i<=nlstate+ndeath;i++)
+     fptt=(*func)(ptt); /* f_3 */
-     for (j=1;j<=nlstate+ndeath;j++){
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-     }
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-   for(h=1; h <=nhstepm; h++){
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-     for(d=1; d <=hstepm; d++){
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-       newm=savm;
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-       /* Covariates have to be included here again */
-       cov[1]=1.;
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line */
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       t= t- del*SQR(fp-fptt);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
-       for (k=1; k<=cptcovage;k++)
+ #ifdef DEBUG
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
-       for (k=1; k<=cptcovprod;k++)
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+       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);
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #endif
-       savm=oldm;
+ #ifdef POWELLDIRECT
-       oldm=newm;
+       if (directest*t < 0.0) { /* Contradiction between both tests */
-     }
+       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
-     for(i=1; i<=nlstate+ndeath; i++)
+       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-       for(j=1;j<=nlstate+ndeath;j++) {
+       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
-         po[i][j][h]=newm[i][j];
+       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+     }
-          */
+       if (directest < 0.0) { /* Then we use it for new direction */
-       }
+ #else
-   } /* end h */
+       if (t < 0.0) { /* Then we use it for new direction */
-   return po;
+ #endif
- }
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
+         for (j=1;j<=n;j++) {
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
- /*************** log-likelihood *************/
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
- double func( double *x)
+         }
- {
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   int i, ii, j, k, mi, d, kk;
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
-   double **out;
+ #ifdef DEBUG
-   double sw; /* Sum of weights */
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   double lli; /* Individual log likelihood */
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   int s1, s2;
+         for(j=1;j<=n;j++){
-   double bbh, survp;
+           printf(" %.12e",xit[j]);
-   long ipmx;
+           fprintf(ficlog," %.12e",xit[j]);
-   /*extern weight */
+         }
-   /* We are differentiating ll according to initial status */
+         printf("\n");
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         fprintf(ficlog,"\n");
-   /*for(i=1;i<imx;i++)
+ #endif
-     printf(" %d\n",s[4][i]);
+       } /* end of t negative */
-   */
+     } /* end if (fptt < fp)  */
-   cov[1]=1.;
+   }
+ }
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   if(mle==1){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ {
-       for(mi=1; mi<= wav[i]-1; mi++){
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+      matrix by transitions matrix until convergence is reached */
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   int i, ii,j,k;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   double min, max, maxmin, maxmax,sumnew=0.;
-           }
+   /* double **matprod2(); */ /* test */
-         for(d=0; d<dh[mi][i]; d++){
+   double **out, cov[NCOVMAX+1], **pmij();
-           newm=savm;
+   double **newm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-           }
+     for (j=1;j<=nlstate+ndeath;j++){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
-           oldm=newm;
+   cov[1]=1.;
-         } /* end mult */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     newm=savm;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     /* Covariates have to be included here again */
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+     cov[2]=agefin;
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     for (k=1; k<=cptcovn;k++) {
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-          * probability in order to take into account the bias as a fraction of the way
+       /*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]]);*/
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+     }
-          * -stepm/2 to stepm/2 .
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-          * For stepm=1 the results are the same as for previous versions of Imach.
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-          * For stepm > 1 the results are less biased than in previous versions.
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-          */
-         s1=s[mw[mi][i]][i];
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-         s2=s[mw[mi+1][i]][i];
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-         bbh=(double)bh[mi][i]/(double)stepm;
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-         /* bias bh is positive if real duration
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-          * is higher than the multiple of stepm and negative otherwise.
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-          */
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-         if( s2 > nlstate){
+     savm=oldm;
-           /* i.e. if s2 is a death state and if the date of death is known
+     oldm=newm;
-              then the contribution to the likelihood is the probability to
+     maxmax=0.;
-              die between last step unit time and current  step unit time,
+     for(j=1;j<=nlstate;j++){
-              which is also equal to probability to die before dh
+       min=1.;
-              minus probability to die before dh-stepm .
+       max=0.;
-              In version up to 0.92 likelihood was computed
+       for(i=1; i<=nlstate; i++) {
-         as if date of death was unknown. Death was treated as any other
+         sumnew=0;
-         health state: the date of the interview describes the actual state
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         and not the date of a change in health state. The former idea was
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-         to consider that at each interview the state was recorded
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-         (healthy, disable or death) and IMaCh was corrected; but when we
+         max=FMAX(max,prlim[i][j]);
-         introduced the exact date of death then we should have modified
+         min=FMIN(min,prlim[i][j]);
-         the contribution of an exact death to the likelihood. This new
+       }
-         contribution is smaller and very dependent of the step unit
+       maxmin=max-min;
-         stepm. It is no more the probability to die between last interview
+       maxmax=FMAX(maxmax,maxmin);
-         and month of death but the probability to survive from last
+     } /* j loop */
-         interview up to one month before death multiplied by the
+     if(maxmax < ftolpl){
-         probability to die within a month. Thanks to Chris
+       return prlim;
-         Jackson for correcting this bug.  Former versions increased
+     }
-         mortality artificially. The bad side is that we add another loop
+   } /* age loop */
-         which slows down the processing. The difference can be up to 10%
+   return prlim; /* should not reach here */
-         lower mortality.
+ }
-           */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ /*************** transition probabilities ***************/
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-         } else if  (s2==-2) {
+ {
-           for (j=1,survp=0. ; j<=nlstate; j++)
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+      computes the probability to be observed in state j being in state i by appying the
-           /*survp += out[s1][j]; */
+      model to the ncovmodel covariates (including constant and age).
-           lli= log(survp);
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         }
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
-         else if  (s2==-4) {
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-           for (j=3,survp=0. ; j<=nlstate; j++)
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-           lli= log(survp);
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         }
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         else if  (s2==-5) {
+   */
-           for (j=1,survp=0. ; j<=2; j++)
+   double s1, lnpijopii;
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   /*double t34;*/
-           lli= log(survp);
+   int i,j, nc, ii, jj;
-         }
+     for(i=1; i<= nlstate; i++){
-         else{
+       for(j=1; j<i;j++){
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*  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 */
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         }
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         /*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); */
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         ipmx +=1;
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         sw += weight[i];
+       }
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       } /* end of wave */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-     } /* end of individual */
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-   }  else if(mle==2){
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         }
-       for(mi=1; mi<= wav[i]-1; mi++){
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       }
-           for (j=1;j<=nlstate+ndeath;j++){
+     }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for(i=1; i<= nlstate; i++){
-           }
+       s1=0;
-         for(d=0; d<=dh[mi][i]; d++){
+       for(j=1; j<i; j++){
-           newm=savm;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-           for (kk=1; kk<=cptcovage;kk++) {
+       }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for(j=i+1; j<=nlstate+ndeath; j++){
-           }
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       }
-           savm=oldm;
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-           oldm=newm;
+       ps[i][i]=1./(s1+1.);
-         } /* end mult */
+       /* Computing other pijs */
+       for(j=1; j<i; j++)
-         s1=s[mw[mi][i]][i];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         s2=s[mw[mi+1][i]][i];
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         bbh=(double)bh[mi][i]/(double)stepm;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         ipmx +=1;
+     } /* end i */
-         sw += weight[i];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       } /* end of wave */
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-     } /* end of individual */
+         ps[ii][jj]=0;
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+         ps[ii][ii]=1;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     }
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-           }
+     /*   } */
-         for(d=0; d<dh[mi][i]; d++){
+     /*   printf("\n "); */
-           newm=savm;
+     /* } */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+     /*
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-           }
+       goto end;*/
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     return ps;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ }
-           savm=oldm;
-           oldm=newm;
+ /**************** Product of 2 matrices ******************/
-         } /* end mult */
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         s1=s[mw[mi][i]][i];
+ {
-         s2=s[mw[mi+1][i]][i];
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-         bbh=(double)bh[mi][i]/(double)stepm;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         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 */
+   /* in, b, out are matrice of pointers which should have been initialized
-         ipmx +=1;
+      before: only the contents of out is modified. The function returns
-         sw += weight[i];
+      a pointer to pointers identical to out */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   int i, j, k;
-       } /* end of wave */
+   for(i=nrl; i<= nrh; i++)
-     } /* end of individual */
+     for(k=ncolol; k<=ncoloh; k++){
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+       out[i][k]=0.;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for(j=ncl; j<=nch; j++)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         out[i][k] +=in[i][j]*b[j][k];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   return out;
-           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);
-           }
+ /************* Higher Matrix Product ***************/
-         for(d=0; d<dh[mi][i]; d++){
-           newm=savm;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ {
-           for (kk=1; kk<=cptcovage;kk++) {
+   /* Computes the transition matrix starting at age 'age' over
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      'nhstepm*hstepm*stepm' months (i.e. until
-           }
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+      (typically every 2 years instead of every month which is too big
-           savm=oldm;
+      for the memory).
-           oldm=newm;
+      Model is determined by parameters x and covariates have to be
-         } /* end mult */
+      included manually here.
-         s1=s[mw[mi][i]][i];
+      */
-         s2=s[mw[mi+1][i]][i];
-         if( s2 > nlstate){
+   int i, j, d, h, k;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   double **out, cov[NCOVMAX+1];
-         }else{
+   double **newm;
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         }
+   /* Hstepm could be zero and should return the unit matrix */
-         ipmx +=1;
+   for (i=1;i<=nlstate+ndeath;i++)
-         sw += weight[i];
+     for (j=1;j<=nlstate+ndeath;j++){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
- /*      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]); */
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-       } /* end of wave */
+     }
-     } /* end of individual */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+   for(h=1; h <=nhstepm; h++){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     for(d=1; d <=hstepm; d++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       newm=savm;
-       for(mi=1; mi<= wav[i]-1; mi++){
+       /* Covariates have to be included here again */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       cov[1]=1.;
-           for (j=1;j<=nlstate+ndeath;j++){
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for (k=1; k<=cptcovn;k++)
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           }
+       for (k=1; k<=cptcovage;k++)
-         for(d=0; d<dh[mi][i]; d++){
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-           newm=savm;
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
+       savm=oldm;
-           oldm=newm;
+       oldm=newm;
-         } /* end mult */
+     }
+     for(i=1; i<=nlstate+ndeath; i++)
-         s1=s[mw[mi][i]][i];
+       for(j=1;j<=nlstate+ndeath;j++) {
-         s2=s[mw[mi+1][i]][i];
+         po[i][j][h]=newm[i][j];
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-         ipmx +=1;
+       }
-         sw += weight[i];
+     /*printf("h=%d ",h);*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   } /* end h */
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+ /*     printf("\n H=%d \n",h); */
-       } /* end of wave */
+   return po;
-     } /* end of individual */
+ }
-   } /* End of if */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ #ifdef NLOPT
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   double fret;
-   return -l;
+   double *xt;
- }
+   int j;
+   myfunc_data *d2 = (myfunc_data *) pd;
- /*************** log-likelihood *************/
+ /* xt = (p1-1); */
- double funcone( double *x)
+   xt=vector(1,n);
- {
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-   /* Same as likeli but slower because of a lot of printf and if */
-   int i, ii, j, k, mi, d, kk;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-   double **out;
+   printf("Function = %.12lf ",fret);
-   double lli; /* Individual log likelihood */
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-   double llt;
+   printf("\n");
-   int s1, s2;
+  free_vector(xt,1,n);
-   double bbh, survp;
+   return fret;
-   /*extern weight */
+ }
-   /* We are differentiating ll according to initial status */
+ #endif
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*for(i=1;i<imx;i++)
+ /*************** log-likelihood *************/
-     printf(" %d\n",s[4][i]);
+ double func( double *x)
-   */
+ {
-   cov[1]=1.;
+   int i, ii, j, k, mi, d, kk;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   double **out;
+   double sw; /* Sum of weights */
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   double lli; /* Individual log likelihood */
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   int s1, s2;
-     for(mi=1; mi<= wav[i]-1; mi++){
+   double bbh, survp;
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+   long ipmx;
-         for (j=1;j<=nlstate+ndeath;j++){
+   /*extern weight */
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* We are differentiating ll according to initial status */
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         }
+   /*for(i=1;i<imx;i++)
-       for(d=0; d<dh[mi][i]; d++){
+     printf(" %d\n",s[4][i]);
-         newm=savm;
+   */
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         for (kk=1; kk<=cptcovage;kk++) {
+   ++countcallfunc;
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         }
+   cov[1]=1.;
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-         savm=oldm;
-         oldm=newm;
+   if(mle==1){
-       } /* end mult */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       /* Computes the values of the ncovmodel covariates of the model
-       s1=s[mw[mi][i]][i];
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-       s2=s[mw[mi+1][i]][i];
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-       bbh=(double)bh[mi][i]/(double)stepm;
+          to be observed in j being in i according to the model.
-       /* bias is positive if real duration
+        */
-        * is higher than the multiple of stepm and negative otherwise.
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-        */
+         cov[2+k]=covar[Tvar[k]][i];
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+       }
-         lli=log(out[s1][s2] - savm[s1][s2]);
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-       } else if  (s2==-2) {
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-         for (j=1,survp=0. ; j<=nlstate; j++)
+          has been calculated etc */
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for(mi=1; mi<= wav[i]-1; mi++){
-         lli= log(survp);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       }else if (mle==1){
+           for (j=1;j<=nlstate+ndeath;j++){
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } else if(mle==2){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+           }
-       } else if(mle==3){  /* exponential inter-extrapolation */
+         for(d=0; d<dh[mi][i]; d++){
-         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 */
+           newm=savm;
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         lli=log(out[s1][s2]); /* Original formula */
+           for (kk=1; kk<=cptcovage;kk++) {
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-         lli=log(out[s1][s2]); /* Original formula */
+           }
-       } /* End of if */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       ipmx +=1;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       sw += weight[i];
+           savm=oldm;
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           oldm=newm;
- /*       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 mult */
-       if(globpr){
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-  %11.6f %11.6f %11.6f ", \
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-           llt +=ll[k]*gipmx/gsw;
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         }
+          * probability in order to take into account the bias as a fraction of the way
-         fprintf(ficresilk," %10.6f\n", -llt);
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-       }
+          * -stepm/2 to stepm/2 .
-     } /* end of wave */
+          * For stepm=1 the results are the same as for previous versions of Imach.
-   } /* end of individual */
+          * For stepm > 1 the results are less biased than in previous versions.
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+          */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         s1=s[mw[mi][i]][i];
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         s2=s[mw[mi+1][i]][i];
-   if(globpr==0){ /* First time we count the contributions and weights */
+         bbh=(double)bh[mi][i]/(double)stepm;
-     gipmx=ipmx;
+         /* bias bh is positive if real duration
-     gsw=sw;
+          * is higher than the multiple of stepm and negative otherwise.
-   }
+          */
-   return -l;
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
- }
+         if( s2 > nlstate){
+           /* i.e. if s2 is a death state and if the date of death is known
+              then the contribution to the likelihood is the probability to
- /*************** function likelione ***********/
+              die between last step unit time and current  step unit time,
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+              which is also equal to probability to die before dh
- {
+              minus probability to die before dh-stepm .
-   /* This routine should help understanding what is done with
+              In version up to 0.92 likelihood was computed
-      the selection of individuals/waves and
+         as if date of death was unknown. Death was treated as any other
-      to check the exact contribution to the likelihood.
+         health state: the date of the interview describes the actual state
-      Plotting could be done.
+         and not the date of a change in health state. The former idea was
-    */
+         to consider that at each interview the state was recorded
-   int k;
+         (healthy, disable or death) and IMaCh was corrected; but when we
+         introduced the exact date of death then we should have modified
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+         the contribution of an exact death to the likelihood. This new
-     strcpy(fileresilk,"ilk");
+         contribution is smaller and very dependent of the step unit
-     strcat(fileresilk,fileres);
+         stepm. It is no more the probability to die between last interview
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+         and month of death but the probability to survive from last
-       printf("Problem with resultfile: %s\n", fileresilk);
+         interview up to one month before death multiplied by the
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+         probability to die within a month. Thanks to Chris
-     }
+         Jackson for correcting this bug.  Former versions increased
-     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");
+         mortality artificially. The bad side is that we add another loop
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+         which slows down the processing. The difference can be up to 10%
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+         lower mortality.
-     for(k=1; k<=nlstate; k++)
+           */
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   }
+         } else if  (s2==-2) {
-   *fretone=(*funcone)(p);
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   if(*globpri !=0){
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     fclose(ficresilk);
+           /*survp += out[s1][j]; */
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+           lli= log(survp);
-     fflush(fichtm);
+         }
-   }
-   return;
+         else if  (s2==-4) {
- }
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           lli= log(survp);
- /*********** Maximum Likelihood Estimation ***************/
+         }
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         else if  (s2==-5) {
- {
+           for (j=1,survp=0. ; j<=2; j++)
-   int i,j, iter;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   double **xi;
+           lli= log(survp);
-   double fret;
+         }
-   double fretone; /* Only one call to likelihood */
-   /*  char filerespow[FILENAMELENGTH];*/
+         else{
-   xi=matrix(1,npar,1,npar);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   for (i=1;i<=npar;i++)
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-     for (j=1;j<=npar;j++)
+         }
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         /*if(lli ==000.0)*/
-   strcpy(filerespow,"pow");
+         /*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); */
-   strcat(filerespow,fileres);
+         ipmx +=1;
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         sw += weight[i];
-     printf("Problem with resultfile: %s\n", filerespow);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+       } /* end of wave */
-   }
+     } /* end of individual */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   }  else if(mle==2){
-   for (i=1;i<=nlstate;i++)
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for(j=1;j<=nlstate+ndeath;j++)
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   fprintf(ficrespow,"\n");
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   free_matrix(xi,1,npar,1,npar);
+           }
-   fclose(ficrespow);
+         for(d=0; d<=dh[mi][i]; d++){
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+           newm=savm;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- /**** Computes Hessian and covariance matrix ***/
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+           savm=oldm;
- {
+           oldm=newm;
-   double  **a,**y,*x,pd;
+         } /* end mult */
-   double **hess;
-   int i, j,jk;
+         s1=s[mw[mi][i]][i];
-   int *indx;
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+         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 */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+         ipmx +=1;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+         sw += weight[i];
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double gompertz(double p[]);
+       } /* end of wave */
-   hess=matrix(1,npar,1,npar);
+     } /* end of individual */
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   for (i=1;i<=npar;i++){
+       for(mi=1; mi<= wav[i]-1; mi++){
-     printf("%d",i);fflush(stdout);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-     /*  printf(" %f ",p[i]);
+         for(d=0; d<dh[mi][i]; d++){
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+           newm=savm;
-   }
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
-   for (i=1;i<=npar;i++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     for (j=1;j<=npar;j++)  {
+           }
-       if (j>i) {
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         printf(".%d%d",i,j);fflush(stdout);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+           savm=oldm;
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+           oldm=newm;
+         } /* end mult */
-         hess[j][i]=hess[i][j];
-         /*printf(" %lf ",hess[i][j]);*/
+         s1=s[mw[mi][i]][i];
-       }
+         s2=s[mw[mi+1][i]][i];
-     }
+         bbh=(double)bh[mi][i]/(double)stepm;
-   }
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   printf("\n");
+         ipmx +=1;
-   fprintf(ficlog,"\n");
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+       } /* end of wave */
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   a=matrix(1,npar,1,npar);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   y=matrix(1,npar,1,npar);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   x=vector(1,npar);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   indx=ivector(1,npar);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   for (i=1;i<=npar;i++)
+           for (j=1;j<=nlstate+ndeath;j++){
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   ludcmp(a,npar,indx,&pd);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   for (j=1;j<=npar;j++) {
+         for(d=0; d<dh[mi][i]; d++){
-     for (i=1;i<=npar;i++) x[i]=0;
+           newm=savm;
-     x[j]=1;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     lubksb(a,npar,indx,x);
+           for (kk=1; kk<=cptcovage;kk++) {
-     for (i=1;i<=npar;i++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       matcov[i][j]=x[i];
+           }
-     }
-   }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   printf("\n#Hessian matrix#\n");
+           savm=oldm;
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+           oldm=newm;
-   for (i=1;i<=npar;i++) {
+         } /* end mult */
-     for (j=1;j<=npar;j++) {
-       printf("%.3e ",hess[i][j]);
+         s1=s[mw[mi][i]][i];
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+         s2=s[mw[mi+1][i]][i];
-     }
+         if( s2 > nlstate){
-     printf("\n");
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     fprintf(ficlog,"\n");
+         }else{
-   }
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         }
-   /* Recompute Inverse */
+         ipmx +=1;
-   for (i=1;i<=npar;i++)
+         sw += weight[i];
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   ludcmp(a,npar,indx,&pd);
+ /*      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 */
-   /*  printf("\n#Hessian matrix recomputed#\n");
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   for (j=1;j<=npar;j++) {
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for (i=1;i<=npar;i++) x[i]=0;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     x[j]=1;
+       for(mi=1; mi<= wav[i]-1; mi++){
-     lubksb(a,npar,indx,x);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1;i<=npar;i++){
+           for (j=1;j<=nlstate+ndeath;j++){
-       y[i][j]=x[i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       printf("%.3e ",y[i][j]);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       fprintf(ficlog,"%.3e ",y[i][j]);
+           }
-     }
+         for(d=0; d<dh[mi][i]; d++){
-     printf("\n");
+           newm=savm;
-     fprintf(ficlog,"\n");
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   }
+           for (kk=1; kk<=cptcovage;kk++) {
-   */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
-   free_matrix(a,1,npar,1,npar);
-   free_matrix(y,1,npar,1,npar);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   free_vector(x,1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   free_ivector(indx,1,npar);
+           savm=oldm;
-   free_matrix(hess,1,npar,1,npar);
+           oldm=newm;
+         } /* end mult */
- }
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
- /*************** hessian matrix ****************/
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+         ipmx +=1;
- {
+         sw += weight[i];
-   int i;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   int l=1, lmax=20;
+         /*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]);*/
-   double k1,k2;
+       } /* end of wave */
-   double p2[NPARMAX+1];
+     } /* end of individual */
-   double res;
+   } /* End of if */
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   double fx;
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   int k=0,kmax=10;
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   double l1;
+   return -l;
+ }
-   fx=func(x);
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+ /*************** log-likelihood *************/
-   for(l=0 ; l <=lmax; l++){
+ double funcone( double *x)
-     l1=pow(10,l);
+ {
-     delts=delt;
+   /* Same as likeli but slower because of a lot of printf and if */
-     for(k=1 ; k <kmax; k=k+1){
+   int i, ii, j, k, mi, d, kk;
-       delt = delta*(l1*k);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-       p2[theta]=x[theta] +delt;
+   double **out;
-       k1=func(p2)-fx;
+   double lli; /* Individual log likelihood */
-       p2[theta]=x[theta]-delt;
+   double llt;
-       k2=func(p2)-fx;
+   int s1, s2;
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   double bbh, survp;
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
- #ifdef DEBUG
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+   /*for(i=1;i<imx;i++)
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+     printf(" %d\n",s[4][i]);
- #endif
+   */
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   cov[1]=1.;
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-         k=kmax;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-       }
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         k=kmax; l=lmax*10.;
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       }
+     for(mi=1; mi<= wav[i]-1; mi++){
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-         delts=delt;
+         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);
-   }
+         }
-   delti[theta]=delts;
+       for(d=0; d<dh[mi][i]; d++){
-   return res;
+         newm=savm;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- }
+         for (kk=1; kk<=cptcovage;kk++) {
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+         }
- {
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   int i;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   int l=1, l1, lmax=20;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   double k1,k2,k3,k4,res,fx;
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-   double p2[NPARMAX+1];
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-   int k;
+         savm=oldm;
+         oldm=newm;
-   fx=func(x);
+       } /* end mult */
-   for (k=1; k<=2; k++) {
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+       s1=s[mw[mi][i]][i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       s2=s[mw[mi+1][i]][i];
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+       bbh=(double)bh[mi][i]/(double)stepm;
-     k1=func(p2)-fx;
+       /* bias is positive if real duration
+        * is higher than the multiple of stepm and negative otherwise.
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+        */
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-     k2=func(p2)-fx;
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     k3=func(p2)-fx;
+         lli= log(survp);
+       }else if (mle==1){
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       } else if(mle==2){
-     k4=func(p2)-fx;
+         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 */
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+       } else if(mle==3){  /* exponential inter-extrapolation */
- #ifdef DEBUG
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-     printf("%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);
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     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);
+         lli=log(out[s1][s2]); /* Original formula */
- #endif
+       } else{  /* mle=0 back to 1 */
-   }
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   return res;
+         /*lli=log(out[s1][s2]); */ /* Original formula */
- }
+       } /* End of if */
+       ipmx +=1;
- /************** Inverse of matrix **************/
+       sw += weight[i];
- void ludcmp(double **a, int n, int *indx, double *d)
+       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]); */
-   int i,imax,j,k;
+       if(globpr){
-   double big,dum,sum,temp;
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-   double *vv;
+  %11.6f %11.6f %11.6f ", \
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-   vv=vector(1,n);
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-   *d=1.0;
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   for (i=1;i<=n;i++) {
+           llt +=ll[k]*gipmx/gsw;
-     big=0.0;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-     for (j=1;j<=n;j++)
+         }
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+         fprintf(ficresilk," %10.6f\n", -llt);
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+       }
-     vv[i]=1.0/big;
+     } /* end of wave */
-   }
+   } /* end of individual */
-   for (j=1;j<=n;j++) {
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     for (i=1;i<j;i++) {
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       sum=a[i][j];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   if(globpr==0){ /* First time we count the contributions and weights */
-       a[i][j]=sum;
+     gipmx=ipmx;
-     }
+     gsw=sw;
-     big=0.0;
+   }
-     for (i=j;i<=n;i++) {
+   return -l;
-       sum=a[i][j];
+ }
-       for (k=1;k<j;k++)
-         sum -= a[i][k]*a[k][j];
-       a[i][j]=sum;
+ /*************** function likelione ***********/
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-         big=dum;
+ {
-         imax=i;
+   /* This routine should help understanding what is done with
-       }
+      the selection of individuals/waves and
-     }
+      to check the exact contribution to the likelihood.
-     if (j != imax) {
+      Plotting could be done.
-       for (k=1;k<=n;k++) {
+    */
-         dum=a[imax][k];
+   int k;
-         a[imax][k]=a[j][k];
-         a[j][k]=dum;
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-       }
+     strcpy(fileresilk,"ilk");
-       *d = -(*d);
+     strcat(fileresilk,fileres);
-       vv[imax]=vv[j];
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-     }
+       printf("Problem with resultfile: %s\n", fileresilk);
-     indx[j]=imax;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+     }
-     if (j != n) {
+     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");
-       dum=1.0/(a[j][j]);
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-       for (i=j+1;i<=n;i++) a[i][j] *= 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]); */
-     }
+     for(k=1; k<=nlstate; k++)
-   }
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   free_vector(vv,1,n);  /* Doesn't work */
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
- ;
+   }
- }
+   *fretone=(*funcone)(p);
- void lubksb(double **a, int n, int *indx, double b[])
+   if(*globpri !=0){
- {
+     fclose(ficresilk);
-   int i,ii=0,ip,j;
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   double sum;
+     fflush(fichtm);
+   }
-   for (i=1;i<=n;i++) {
+   return;
-     ip=indx[i];
+ }
-     sum=b[ip];
-     b[ip]=b[i];
-     if (ii)
+ /*********** Maximum Likelihood Estimation ***************/
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-     else if (sum) ii=i;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-     b[i]=sum;
+ {
-   }
+   int i,j, iter=0;
-   for (i=n;i>=1;i--) {
+   double **xi;
-     sum=b[i];
+   double fret;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   double fretone; /* Only one call to likelihood */
-     b[i]=sum/a[i][i];
+   /*  char filerespow[FILENAMELENGTH];*/
-   }
- }
+ #ifdef NLOPT
+   int creturn;
- void pstamp(FILE *fichier)
+   nlopt_opt opt;
- {
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   double *lb;
- }
+   double minf; /* the minimum objective value, upon return */
+   double * p1; /* Shifted parameters from 0 instead of 1 */
- /************ Frequencies ********************/
+   myfunc_data dinst, *d = &dinst;
- 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[])
+ #endif
- {  /* Some frequencies */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   xi=matrix(1,npar,1,npar);
-   int first;
+   for (i=1;i<=npar;i++)
-   double ***freq; /* Frequencies */
+     for (j=1;j<=npar;j++)
-   double *pp, **prop;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   char fileresp[FILENAMELENGTH];
+   strcpy(filerespow,"pow");
+   strcat(filerespow,fileres);
-   pp=vector(1,nlstate);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     printf("Problem with resultfile: %s\n", filerespow);
-   strcpy(fileresp,"p");
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   strcat(fileresp,fileres);
+   }
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   for (i=1;i<=nlstate;i++)
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+     for(j=1;j<=nlstate+ndeath;j++)
-     exit(0);
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   }
+   fprintf(ficrespow,"\n");
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+ #ifdef POWELL
-   j1=0;
+   powell(p,xi,npar,ftol,&iter,&fret,func);
+ #endif
-   j=cptcoveff;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+ #ifdef NLOPT
+ #ifdef NEWUOA
-   first=1;
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
-   for(k1=1; k1<=j;k1++){
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-     for(i1=1; i1<=ncodemax[k1];i1++){
+ #endif
-       j1++;
+   lb=vector(0,npar-1);
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-         scanf("%d", i);*/
+   nlopt_set_lower_bounds(opt, lb);
-       for (i=-5; i<=nlstate+ndeath; i++)
+   nlopt_set_initial_step1(opt, 0.1);
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           for(m=iagemin; m <= iagemax+3; m++)
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-             freq[i][jk][m]=0;
+   d->function = func;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-     for (i=1; i<=nlstate; i++)
+   nlopt_set_min_objective(opt, myfunc, d);
-       for(m=iagemin; m <= iagemax+3; m++)
+   nlopt_set_xtol_rel(opt, ftol);
-         prop[i][m]=0;
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+     printf("nlopt failed! %d\n",creturn);
-       dateintsum=0;
+   }
-       k2cpt=0;
+   else {
-       for (i=1; i<=imx; i++) {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-         bool=1;
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-         if  (cptcovn>0) {
+     iter=1; /* not equal */
-           for (z1=1; z1<=cptcoveff; z1++)
+   }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   nlopt_destroy(opt);
-               bool=0;
+ #endif
-         }
+   free_matrix(xi,1,npar,1,npar);
-         if (bool==1){
+   fclose(ficrespow);
-           for(m=firstpass; m<=lastpass; m++){
+   printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-             k2=anint[m][i]+(mint[m][i]/12.);
+   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+ }
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               if (m<lastpass) {
+ /**** Computes Hessian and covariance matrix ***/
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+ {
-               }
+   double  **a,**y,*x,pd;
+   double **hess;
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+   int i, j;
-                 dateintsum=dateintsum+k2;
+   int *indx;
-                 k2cpt++;
-               }
+   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);
-           }
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-         }
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-       }
+   double gompertz(double p[]);
+   hess=matrix(1,npar,1,npar);
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-       if  (cptcovn>0) {
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-         fprintf(ficresp, "\n#********** Variable ");
+   for (i=1;i<=npar;i++){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     printf("%d",i);fflush(stdout);
-         fprintf(ficresp, "**********\n#");
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-       }
-       for(i=1; i<=nlstate;i++)
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresp, "\n");
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-       for(i=iagemin; i <= iagemax+3; i++){
+   }
-         if(i==iagemax+3){
-           fprintf(ficlog,"Total");
+   for (i=1;i<=npar;i++) {
-         }else{
+     for (j=1;j<=npar;j++)  {
-           if(first==1){
+       if (j>i) {
-             first=0;
+         printf(".%d%d",i,j);fflush(stdout);
-             printf("See log file for details...\n");
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-           }
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-           fprintf(ficlog,"Age %d", i);
-         }
+         hess[j][i]=hess[i][j];
-         for(jk=1; jk <=nlstate ; jk++){
+         /*printf(" %lf ",hess[i][j]);*/
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       }
-             pp[jk] += freq[jk][m][i];
+     }
-         }
+   }
-         for(jk=1; jk <=nlstate ; jk++){
+   printf("\n");
-           for(m=-1, pos=0; m <=0 ; m++)
+   fprintf(ficlog,"\n");
-             pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10){
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-             if(first==1){
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             }
+   a=matrix(1,npar,1,npar);
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   y=matrix(1,npar,1,npar);
-           }else{
+   x=vector(1,npar);
-             if(first==1)
+   indx=ivector(1,npar);
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (i=1;i<=npar;i++)
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-           }
+   ludcmp(a,npar,indx,&pd);
-         }
+   for (j=1;j<=npar;j++) {
-         for(jk=1; jk <=nlstate ; jk++){
+     for (i=1;i<=npar;i++) x[i]=0;
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+     x[j]=1;
-             pp[jk] += freq[jk][m][i];
+     lubksb(a,npar,indx,x);
-         }
+     for (i=1;i<=npar;i++){
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+       matcov[i][j]=x[i];
-           pos += pp[jk];
+     }
-           posprop += prop[jk][i];
+   }
-         }
-         for(jk=1; jk <=nlstate ; jk++){
+   printf("\n#Hessian matrix#\n");
-           if(pos>=1.e-5){
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-             if(first==1)
+   for (i=1;i<=npar;i++) {
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     for (j=1;j<=npar;j++) {
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+       printf("%.3e ",hess[i][j]);
-           }else{
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-             if(first==1)
+     }
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+     printf("\n");
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+     fprintf(ficlog,"\n");
-           }
+   }
-           if( i <= iagemax){
-             if(pos>=1.e-5){
+   /* Recompute Inverse */
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   for (i=1;i<=npar;i++)
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+   ludcmp(a,npar,indx,&pd);
-             }
-             else
+   /*  printf("\n#Hessian matrix recomputed#\n");
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-           }
+   for (j=1;j<=npar;j++) {
-         }
+     for (i=1;i<=npar;i++) x[i]=0;
+     x[j]=1;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+     lubksb(a,npar,indx,x);
-           for(m=-1; m <=nlstate+ndeath; m++)
+     for (i=1;i<=npar;i++){
-             if(freq[jk][m][i] !=0 ) {
+       y[i][j]=x[i];
-             if(first==1)
+       printf("%.3e ",y[i][j]);
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+       fprintf(ficlog,"%.3e ",y[i][j]);
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+     }
-             }
+     printf("\n");
-         if(i <= iagemax)
+     fprintf(ficlog,"\n");
-           fprintf(ficresp,"\n");
+   }
-         if(first==1)
+   */
-           printf("Others in log...\n");
-         fprintf(ficlog,"\n");
+   free_matrix(a,1,npar,1,npar);
-       }
+   free_matrix(y,1,npar,1,npar);
-     }
+   free_vector(x,1,npar);
-   }
+   free_ivector(indx,1,npar);
-   dateintmean=dateintsum/k2cpt;
+   free_matrix(hess,1,npar,1,npar);
-   fclose(ficresp);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+ }
-   free_vector(pp,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+ /*************** hessian matrix ****************/
-   /* End of Freq */
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- }
+ {
+   int i;
- /************ Prevalence ********************/
+   int l=1, lmax=20;
- 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)
+   double k1,k2;
- {
+   double p2[MAXPARM+1]; /* identical to x */
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   double res;
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-      We still use firstpass and lastpass as another selection.
+   double fx;
-   */
+   int k=0,kmax=10;
+   double l1;
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
-   double ***freq; /* Frequencies */
+   fx=func(x);
-   double *pp, **prop;
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   double pos,posprop;
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   double  y2; /* in fractional years */
+     l1=pow(10,l);
-   int iagemin, iagemax;
+     delts=delt;
+     for(k=1 ; k <kmax; k=k+1){
-   iagemin= (int) agemin;
+       delt = delta*(l1*k);
-   iagemax= (int) agemax;
+       p2[theta]=x[theta] +delt;
-   /*pp=vector(1,nlstate);*/
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       p2[theta]=x[theta]-delt;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+       k2=func(p2)-fx;
-   j1=0;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   j=cptcoveff;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+ #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);
-   for(k1=1; k1<=j;k1++){
+       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(i1=1; i1<=ncodemax[k1];i1++){
+ #endif
-       j1++;
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-       for (i=1; i<=nlstate; i++)
+         k=kmax;
-         for(m=iagemin; m <= iagemax+3; m++)
+       }
-           prop[i][m]=0.0;
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+         k=kmax; l=lmax*10;
-       for (i=1; i<=imx; i++) { /* Each individual */
+       }
-         bool=1;
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-         if  (cptcovn>0) {
+         delts=delt;
-           for (z1=1; z1<=cptcoveff; z1++)
+       }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     }
-               bool=0;
+   }
-         }
+   delti[theta]=delts;
-         if (bool==1) {
+   return res;
-           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;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-               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);
+   int i;
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+   int l=1, lmax=20;
-                 /*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]]);*/
+   double k1,k2,k3,k4,res,fx;
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   double p2[MAXPARM+1];
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   int k;
-               }
-             }
+   fx=func(x);
-           } /* end selection of waves */
+   for (k=1; k<=2; k++) {
-         }
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-       }
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-       for(i=iagemin; i <= iagemax+3; i++){
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     k1=func(p2)-fx;
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-           posprop += prop[jk][i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-         }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     k2=func(p2)-fx;
-         for(jk=1; jk <=nlstate ; jk++){
-           if( i <=  iagemax){
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-             if(posprop>=1.e-5){
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+     k3=func(p2)-fx;
-             }
-           }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-         }/* end jk */
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-       }/* end i */
+     k4=func(p2)-fx;
-     } /* end i1 */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-   } /* end k1 */
+ #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);
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+     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);
-   /*free_vector(pp,1,nlstate);*/
+ #endif
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   }
- }  /* End of prevalence */
+   return res;
+ }
- /************* Waves Concatenation ***************/
+ /************** Inverse of matrix **************/
- 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)
+ void ludcmp(double **a, int n, int *indx, double *d)
  {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   int i,imax,j,k;
-      Death is a valid wave (if date is known).
+   double big,dum,sum,temp;
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+   double *vv;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-      and mw[mi+1][i]. dh depends on stepm.
+   vv=vector(1,n);
-      */
+   *d=1.0;
+   for (i=1;i<=n;i++) {
-   int i, mi, m;
+     big=0.0;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+     for (j=1;j<=n;j++)
-      double sum=0., jmean=0.;*/
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-   int first;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-   int j, k=0,jk, ju, jl;
+     vv[i]=1.0/big;
-   double sum=0.;
+   }
-   first=0;
+   for (j=1;j<=n;j++) {
-   jmin=1e+5;
+     for (i=1;i<j;i++) {
-   jmax=-1;
+       sum=a[i][j];
-   jmean=0.;
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-   for(i=1; i<=imx; i++){
+       a[i][j]=sum;
-     mi=0;
+     }
-     m=firstpass;
+     big=0.0;
-     while(s[m][i] <= nlstate){
+     for (i=j;i<=n;i++) {
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       sum=a[i][j];
-         mw[++mi][i]=m;
+       for (k=1;k<j;k++)
-       if(m >=lastpass)
+         sum -= a[i][k]*a[k][j];
-         break;
+       a[i][j]=sum;
-       else
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-         m++;
+         big=dum;
-     }/* end while */
+         imax=i;
-     if (s[m][i] > nlstate){
+       }
-       mi++;     /* Death is another wave */
+     }
-       /* if(mi==0)  never been interviewed correctly before death */
+     if (j != imax) {
-          /* Only death is a correct wave */
+       for (k=1;k<=n;k++) {
-       mw[mi][i]=m;
+         dum=a[imax][k];
-     }
+         a[imax][k]=a[j][k];
+         a[j][k]=dum;
-     wav[i]=mi;
+       }
-     if(mi==0){
+       *d = -(*d);
-       nbwarn++;
+       vv[imax]=vv[j];
-       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);
+     indx[j]=imax;
-         first=1;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-       }
+     if (j != n) {
-       if(first==1){
+       dum=1.0/(a[j][j]);
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-       }
+     }
-     } /* end mi==0 */
+   }
-   } /* End individuals */
+   free_vector(vv,1,n);  /* Doesn't work */
+ ;
-   for(i=1; i<=imx; i++){
+ }
-     for(mi=1; mi<wav[i];mi++){
-       if (stepm <=0)
+ void lubksb(double **a, int n, int *indx, double b[])
-         dh[mi][i]=1;
+ {
-       else{
+   int i,ii=0,ip,j;
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+   double sum;
-           if (agedc[i] < 2*AGESUP) {
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+   for (i=1;i<=n;i++) {
-             if(j==0) j=1;  /* Survives at least one month after exam */
+     ip=indx[i];
-             else if(j<0){
+     sum=b[ip];
-               nberr++;
+     b[ip]=b[i];
-               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]);
+     if (ii)
-               j=1; /* Temporary Dangerous patch */
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-               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);
+     else if (sum) ii=i;
-               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]);
+     b[i]=sum;
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   }
-             }
+   for (i=n;i>=1;i--) {
-             k=k+1;
+     sum=b[i];
-             if (j >= jmax){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-               jmax=j;
+     b[i]=sum/a[i][i];
-               ijmax=i;
+   }
-             }
+ }
-             if (j <= jmin){
-               jmin=j;
+ void pstamp(FILE *fichier)
-               ijmin=i;
+ {
-             }
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-             sum=sum+j;
+ }
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ /************ Frequencies ********************/
-           }
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-         }
+ {  /* Some frequencies */
-         else{
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   int i, m, jk, j1, bool, z1,j;
- /*        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]); */
+   int first;
+   double ***freq; /* Frequencies */
-           k=k+1;
+   double *pp, **prop;
-           if (j >= jmax) {
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-             jmax=j;
+   char fileresp[FILENAMELENGTH];
-             ijmax=i;
-           }
+   pp=vector(1,nlstate);
-           else if (j <= jmin){
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-             jmin=j;
+   strcpy(fileresp,"p");
-             ijmin=i;
+   strcat(fileresp,fileres);
-           }
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-           /*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]);*/
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-           if(j<0){
+     exit(0);
-             nberr++;
+   }
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-             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]);
+   j1=0;
-           }
-           sum=sum+j;
+   j=cptcoveff;
-         }
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-         jk= j/stepm;
-         jl= j -jk*stepm;
+   first=1;
-         ju= j -(jk+1)*stepm;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-           if(jl==0){
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
-             dh[mi][i]=jk;
+   /*    j1++; */
-             bh[mi][i]=0;
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-           }else{ /* We want a negative bias in order to only have interpolation ie
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-                   * at the price of an extra matrix product in likelihood */
+         scanf("%d", i);*/
-             dh[mi][i]=jk+1;
+       for (i=-5; i<=nlstate+ndeath; i++)
-             bh[mi][i]=ju;
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           }
+           for(m=iagemin; m <= iagemax+3; m++)
-         }else{
+             freq[i][jk][m]=0;
-           if(jl <= -ju){
-             dh[mi][i]=jk;
+       for (i=1; i<=nlstate; i++)
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         for(m=iagemin; m <= iagemax+3; m++)
-                                  * is higher than the multiple of stepm and negative otherwise.
+           prop[i][m]=0;
-                                  */
-           }
+       dateintsum=0;
-           else{
+       k2cpt=0;
-             dh[mi][i]=jk+1;
+       for (i=1; i<=imx; i++) {
-             bh[mi][i]=ju;
+         bool=1;
-           }
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-           if(dh[mi][i]==0){
+           for (z1=1; z1<=cptcoveff; z1++)
-             dh[mi][i]=1; /* At least one step */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-             bh[mi][i]=ju; /* At least one step */
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-             /*  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);*/
+               bool=0;
-           }
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-         } /* end if mle */
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-       }
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-     } /* end wave */
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-   }
+             }
-   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);
+         if (bool==1){
-  }
+           for(m=firstpass; m<=lastpass; m++){
+             k2=anint[m][i]+(mint[m][i]/12.);
- /*********** Tricode ****************************/
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
- void tricode(int *Tvar, int **nbcode, int imx)
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
- {
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+               if (m<lastpass) {
-   int cptcode=0;
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-   cptcoveff=0;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+               }
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+                 dateintsum=dateintsum+k2;
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+                 k2cpt++;
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+               }
-                                modality*/
+               /*}*/
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+           }
-       Ndum[ij]++; /*store the modality */
+         }
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       } /* end i */
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
-                                        Tvar[j]. If V=sex and male is 0 and
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-                                        female is 1, then  cptcode=1.*/
+       pstamp(ficresp);
-     }
+       if  (cptcovn>0) {
+         fprintf(ficresp, "\n#********** Variable ");
-     for (i=0; i<=cptcode; i++) {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       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(ficresp, "**********\n#");
-     }
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-     ij=1;
+         fprintf(ficlog, "**********\n#");
-     for (i=1; i<=ncodemax[j]; i++) {
+       }
-       for (k=0; k<= maxncov; k++) {
+       for(i=1; i<=nlstate;i++)
-         if (Ndum[k] != 0) {
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-           nbcode[Tvar[j]][ij]=k;
+       fprintf(ficresp, "\n");
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+       for(i=iagemin; i <= iagemax+3; i++){
-           ij++;
+         if(i==iagemax+3){
-         }
+           fprintf(ficlog,"Total");
-         if (ij > ncodemax[j]) break;
+         }else{
-       }
+           if(first==1){
-     }
+             first=0;
-   }
+             printf("See log file for details...\n");
+           }
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+           fprintf(ficlog,"Age %d", i);
+         }
-  for (i=1; i<=ncovmodel-2; i++) {
+         for(jk=1; jk <=nlstate ; jk++){
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-    ij=Tvar[i];
+             pp[jk] += freq[jk][m][i];
-    Ndum[ij]++;
+         }
-  }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-  ij=1;
+             pos += freq[jk][m][i];
-  for (i=1; i<= maxncov; i++) {
+           if(pp[jk]>=1.e-10){
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+             if(first==1){
-      Tvaraff[ij]=i; /*For printing */
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-      ij++;
+             }
-    }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-  }
+           }else{
+             if(first==1)
-  cptcoveff=ij-1; /*Number of simple covariates*/
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- }
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
- /*********** Health Expectancies ****************/
+         }
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
- {
+             pp[jk] += freq[jk][m][i];
-   /* Health expectancies, no variances */
+         }
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-   double age, agelim, hf;
+           pos += pp[jk];
-   double ***p3mat;
+           posprop += prop[jk][i];
-   double eip;
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-   pstamp(ficreseij);
+           if(pos>=1.e-5){
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+             if(first==1)
-   fprintf(ficreseij,"# Age");
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   for(i=1; i<=nlstate;i++){
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-     for(j=1; j<=nlstate;j++){
+           }else{
-       fprintf(ficreseij," e%1d%1d ",i,j);
+             if(first==1)
-     }
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-     fprintf(ficreseij," e%1d. ",i);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   }
+           }
-   fprintf(ficreseij,"\n");
+           if( i <= iagemax){
+             if(pos>=1.e-5){
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   if(estepm < stepm){
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   }
+             }
-   else  hstepm=estepm;
+             else
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-    * This is mainly to measure the difference between two models: for example
+           }
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+         }
-    * we are calculating an estimate of the Life Expectancy assuming a linear
-    * progression in between and thus overestimating or underestimating according
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-    * to the curvature of the survival function. If, for the same date, we
+           for(m=-1; m <=nlstate+ndeath; m++)
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+             if(freq[jk][m][i] !=0 ) {
-    * to compare the new estimate of Life expectancy with the same linear
+             if(first==1)
-    * hypothesis. A more precise result, taking into account a more precise
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-    * curvature will be obtained if estepm is as small as stepm. */
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
-   /* For example we decided to compute the life expectancy with the smallest unit */
+         if(i <= iagemax)
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+           fprintf(ficresp,"\n");
-      nhstepm is the number of hstepm from age to agelim
+         if(first==1)
-      nstepm is the number of stepm from age to agelin.
+           printf("Others in log...\n");
-      Look at hpijx to understand the reason of that which relies in memory size
+         fprintf(ficlog,"\n");
-      and note for a fixed period like estepm months */
+       }
-   /* 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
+   dateintmean=dateintsum/k2cpt;
-      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.
+   fclose(ficresp);
-   */
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   free_vector(pp,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-   agelim=AGESUP;
+   /* End of Freq */
-   /* If stepm=6 months */
+ }
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+ /************ Prevalence ********************/
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
- /* nhstepm age range expressed in number of stepm */
+ {
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-   /* if (stepm >= YEARM) hstepm=1;*/
+      We still use firstpass and lastpass as another selection.
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   */
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int i, m, jk, j1, bool, z1,j;
-   for (age=bage; age<=fage; age ++){
+   double **prop;
+   double posprop;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   double  y2; /* in fractional years */
+   int iagemin, iagemax;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   int first; /** to stop verbosity which is redirected to log file */
-     printf("%d|",(int)age);fflush(stdout);
+   iagemin= (int) agemin;
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   iagemax= (int) agemax;
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-     /* Computing expectancies */
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-     for(i=1; i<=nlstate;i++)
+   j1=0;
-       for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   /*j=cptcoveff;*/
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+   if (cptcovn<1) {j=1;ncodemax[1]=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]);*/
+   first=1;
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-         }
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
+       j1++;*/
-     fprintf(ficreseij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++){
+       for (i=1; i<=nlstate; i++)
-       eip=0;
+         for(m=iagemin; m <= iagemax+3; m++)
-       for(j=1; j<=nlstate;j++){
+           prop[i][m]=0.0;
-         eip +=eij[i][j][(int)age];
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       for (i=1; i<=imx; i++) { /* Each individual */
-       }
+         bool=1;
-       fprintf(ficreseij,"%9.4f", eip );
+         if  (cptcovn>0) {
-     }
+           for (z1=1; z1<=cptcoveff; z1++)
-     fprintf(ficreseij,"\n");
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               bool=0;
-   }
+         }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if (bool==1) {
-   printf("\n");
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   fprintf(ficlog,"\n");
+             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;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
- 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((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
- {
+                 /*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]]);*/
-   /* Covariances of health expectancies eij and of total life expectancies according
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-    to initial status i, ei. .
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   */
+               }
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+             }
-   double age, agelim, hf;
+           } /* end selection of waves */
-   double ***p3matp, ***p3matm, ***varhe;
+         }
-   double **dnewm,**doldm;
+       }
-   double *xp, *xm;
+       for(i=iagemin; i <= iagemax+3; i++){
-   double **gp, **gm;
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   double ***gradg, ***trgradg;
+           posprop += prop[jk][i];
-   int theta;
+         }
-   double eip, vip;
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <=  iagemax){
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+             if(posprop>=1.e-5){
-   xp=vector(1,npar);
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-   xm=vector(1,npar);
+             } else{
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+               if(first==1){
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+                 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]);
-   pstamp(ficresstdeij);
+               }
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+             }
-   fprintf(ficresstdeij,"# Age");
+           }
-   for(i=1; i<=nlstate;i++){
+         }/* end jk */
-     for(j=1; j<=nlstate;j++)
+       }/* end i */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     /*} *//* end i1 */
-     fprintf(ficresstdeij," e%1d. ",i);
+   } /* end j1 */
-   }
-   fprintf(ficresstdeij,"\n");
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*free_vector(pp,1,nlstate);*/
-   pstamp(ficrescveij);
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+ }  /* End of prevalence */
-   fprintf(ficrescveij,"# Age");
-   for(i=1; i<=nlstate;i++)
+ /************* Waves Concatenation ***************/
-     for(j=1; j<=nlstate;j++){
-       cptj= (j-1)*nlstate+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)
-       for(i2=1; i2<=nlstate;i2++)
+ {
-         for(j2=1; j2<=nlstate;j2++){
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-           cptj2= (j2-1)*nlstate+i2;
+      Death is a valid wave (if date is known).
-           if(cptj2 <= cptj)
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-         }
+      and mw[mi+1][i]. dh depends on stepm.
-     }
+      */
-   fprintf(ficrescveij,"\n");
+   int i, mi, m;
-   if(estepm < stepm){
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+      double sum=0., jmean=0.;*/
-   }
+   int first;
-   else  hstepm=estepm;
+   int j, k=0,jk, ju, jl;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   double sum=0.;
-    * This is mainly to measure the difference between two models: for example
+   first=0;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   jmin=100000;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   jmax=-1;
-    * progression in between and thus overestimating or underestimating according
+   jmean=0.;
-    * to the curvature of the survival function. If, for the same date, we
+   for(i=1; i<=imx; i++){
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+     mi=0;
-    * to compare the new estimate of Life expectancy with the same linear
+     m=firstpass;
-    * hypothesis. A more precise result, taking into account a more precise
+     while(s[m][i] <= nlstate){
-    * curvature will be obtained if estepm is as small as stepm. */
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+         mw[++mi][i]=m;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+       if(m >=lastpass)
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+         break;
-      nhstepm is the number of hstepm from age to agelim
+       else
-      nstepm is the number of stepm from age to agelin.
+         m++;
-      Look at hpijx to understand the reason of that which relies in memory size
+     }/* end while */
-      and note for a fixed period like estepm months */
+     if (s[m][i] > nlstate){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       mi++;     /* Death is another wave */
-      survival function given by stepm (the optimization length). Unfortunately it
+       /* if(mi==0)  never been interviewed correctly before death */
-      means that if the survival funtion is printed only each two years of age and if
+          /* Only death is a correct wave */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       mw[mi][i]=m;
-      results. So we changed our mind and took the option of the best precision.
+     }
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     wav[i]=mi;
+     if(mi==0){
-   /* If stepm=6 months */
+       nbwarn++;
-   /* nhstepm age range expressed in number of stepm */
+       if(first==0){
-   agelim=AGESUP;
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         first=1;
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+       }
-   /* if (stepm >= YEARM) hstepm=1;*/
+       if(first==1){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       }
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     } /* end mi==0 */
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   } /* End individuals */
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+   for(i=1; i<=imx; i++){
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+     for(mi=1; mi<wav[i];mi++){
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+       if (stepm <=0)
+         dh[mi][i]=1;
-   for (age=bage; age<=fage; age ++){
+       else{
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           if (agedc[i] < 2*AGESUP) {
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             else if(j<0){
+               nberr++;
-     /* Computing  Variances of health expectancies */
+               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]);
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+               j=1; /* Temporary Dangerous patch */
-        decrease memory allocation */
+               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);
-     for(theta=1; theta <=npar; theta++){
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-       for(i=1; i<=npar; 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);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+             }
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+             k=k+1;
-       }
+             if (j >= jmax){
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+               jmax=j;
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+               ijmax=i;
+             }
-       for(j=1; j<= nlstate; j++){
+             if (j <= jmin){
-         for(i=1; i<=nlstate; i++){
+               jmin=j;
-           for(h=0; h<=nhstepm-1; h++){
+               ijmin=i;
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             }
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+             sum=sum+j;
-           }
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-         }
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-       }
+           }
+         }
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+         else{
-         for(h=0; h<=nhstepm-1; h++){
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-         }
-     }/* End theta */
+           k=k+1;
+           if (j >= jmax) {
+             jmax=j;
-     for(h=0; h<=nhstepm-1; h++)
+             ijmax=i;
-       for(j=1; j<=nlstate*nlstate;j++)
+           }
-         for(theta=1; theta <=npar; theta++)
+           else if (j <= jmin){
-           trgradg[h][j][theta]=gradg[h][theta][j];
+             jmin=j;
+             ijmin=i;
+           }
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+           /*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]);*/
-         varhe[ij][ji][(int)age] =0.;
+           if(j<0){
+             nberr++;
-      printf("%d|",(int)age);fflush(stdout);
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-      for(h=0;h<=nhstepm-1;h++){
+           }
-       for(k=0;k<=nhstepm-1;k++){
+           sum=sum+j;
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+         }
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+         jk= j/stepm;
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+         jl= j -jk*stepm;
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+         ju= j -(jk+1)*stepm;
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-       }
+           if(jl==0){
-     }
+             dh[mi][i]=jk;
+             bh[mi][i]=0;
-     /* Computing expectancies */
+           }else{ /* We want a negative bias in order to only have interpolation ie
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+                   * to avoid the price of an extra matrix product in likelihood */
-     for(i=1; i<=nlstate;i++)
+             dh[mi][i]=jk+1;
-       for(j=1; j<=nlstate;j++)
+             bh[mi][i]=ju;
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           }
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+         }else{
+           if(jl <= -ju){
-           /* 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]);*/
+             dh[mi][i]=jk;
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         }
+                                  * is higher than the multiple of stepm and negative otherwise.
+                                  */
-     fprintf(ficresstdeij,"%3.0f",age );
+           }
-     for(i=1; i<=nlstate;i++){
+           else{
-       eip=0.;
+             dh[mi][i]=jk+1;
-       vip=0.;
+             bh[mi][i]=ju;
-       for(j=1; j<=nlstate;j++){
+           }
-         eip += eij[i][j][(int)age];
+           if(dh[mi][i]==0){
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+             dh[mi][i]=1; /* At least one step */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+             bh[mi][i]=ju; /* At least one step */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-       }
+           }
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+         } /* end if mle */
-     }
+       }
-     fprintf(ficresstdeij,"\n");
+     } /* end wave */
+   }
-     fprintf(ficrescveij,"%3.0f",age );
+   jmean=sum/k;
-     for(i=1; i<=nlstate;i++)
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-       for(j=1; j<=nlstate;j++){
+   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);
-         cptj= (j-1)*nlstate+i;
+  }
-         for(i2=1; i2<=nlstate;i2++)
-           for(j2=1; j2<=nlstate;j2++){
+ /*********** Tricode ****************************/
-             cptj2= (j2-1)*nlstate+i2;
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-             if(cptj2 <= cptj)
+ {
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-           }
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-       }
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-     fprintf(ficrescveij,"\n");
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+    * nbcode[Tvar[j]][1]=
-   }
+   */
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   int modmaxcovj=0; /* Modality max of covariates j */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   int cptcode=0; /* Modality max of covariates j */
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int modmincovj=0; /* Modality min of covariates j */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   printf("\n");
-   fprintf(ficlog,"\n");
+   cptcoveff=0;
-   free_vector(xm,1,npar);
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   free_vector(xp,1,npar);
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   /* Loop on covariates without age and products */
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
- }
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
+                                modality of this covariate Vj*/
- /************ Variance ******************/
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+                                     * If product of Vn*Vm, still boolean *:
- {
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   /* Variance of health expectancies */
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   /* double **newm;*/
+                                       modality of the nth covariate of individual i. */
-   double **dnewm,**doldm;
+       if (ij > modmaxcovj)
-   double **dnewmp,**doldmp;
+         modmaxcovj=ij;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+       else if (ij < modmincovj)
-   int k, cptcode;
+         modmincovj=ij;
-   double *xp;
+       if ((ij < -1) && (ij > NCOVMAX)){
-   double **gp, **gm;  /* for var eij */
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   double ***gradg, ***trgradg; /*for var eij */
+         exit(1);
-   double **gradgp, **trgradgp; /* for var p point j */
+       }else
-   double *gpp, *gmp; /* for var p point j */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   double ***p3mat;
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-   double age,agelim, hf;
+       /* getting the maximum value of the modality of the covariate
-   double ***mobaverage;
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   int theta;
+          female is 1, then modmaxcovj=1.*/
-   char digit[4];
+     }
-   char digitp[25];
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+     cptcode=modmaxcovj;
-   char fileresprobmorprev[FILENAMELENGTH];
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+    /*for (i=0; i<=cptcode; i++) {*/
-   if(popbased==1){
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-     if(mobilav!=0)
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-       strcpy(digitp,"-populbased-mobilav-");
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-     else strcpy(digitp,"-populbased-nomobil-");
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-   }
+       }
-   else
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-     strcpy(digitp,"-stablbased-");
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+        modmincovj=3; modmaxcovj = 7;
-     }
+        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
+        variables V1_1 and V1_2.
-   strcpy(fileresprobmorprev,"prmorprev");
+        nbcode[Tvar[j]][ij]=k;
-   sprintf(digit,"%-d",ij);
+        nbcode[Tvar[j]][1]=0;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+        nbcode[Tvar[j]][2]=1;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+        nbcode[Tvar[j]][3]=2;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+     */
-   strcat(fileresprobmorprev,fileres);
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+         /*recode from 0 */
-   }
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      k is a modality. If we have model=V1+V1*sex
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-   pstamp(ficresprobmorprev);
+           ij++;
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+         }
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+         if (ij > ncodemax[j]) break;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       }  /* end of loop on */
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+     } /* end of loop on modality */
-     for(i=1; i<=nlstate;i++)
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficgp,"\n# Routine varevsij");
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-   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");
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+    Ndum[ij]++;
- /*   } */
+  }
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   pstamp(ficresvij);
+  ij=1;
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-   if(popbased==1)
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-   else
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+      Tvaraff[ij]=i; /*For printing (unclear) */
-   fprintf(ficresvij,"# Age");
+      ij++;
-   for(i=1; i<=nlstate;i++)
+    }else
-     for(j=1; j<=nlstate;j++)
+        Tvaraff[ij]=0;
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+  }
-   fprintf(ficresvij,"\n");
+  ij--;
+  cptcoveff=ij; /*Number of total covariates*/
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+ }
-   doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ /*********** Health Expectancies ****************/
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   gpp=vector(nlstate+1,nlstate+ndeath);
-   gmp=vector(nlstate+1,nlstate+ndeath);
+ {
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm;
-   if(estepm < stepm){
+   int nhstepma, nstepma; /* Decreasing with age */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   double age, agelim, hf;
-   }
+   double ***p3mat;
-   else  hstepm=estepm;
+   double eip;
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   pstamp(ficreseij);
-      nhstepm is the number of hstepm from age to agelim
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-      nstepm is the number of stepm from age to agelin.
+   fprintf(ficreseij,"# Age");
-      Look at hpijx to understand the reason of that which relies in memory size
+   for(i=1; i<=nlstate;i++){
-      and note for a fixed period like k years */
+     for(j=1; j<=nlstate;j++){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       fprintf(ficreseij," e%1d%1d ",i,j);
-      survival function given by stepm (the optimization length). Unfortunately it
+     }
-      means that if the survival funtion is printed every two years of age and if
+     fprintf(ficreseij," e%1d. ",i);
-      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.
+   fprintf(ficreseij,"\n");
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
+   if(estepm < stepm){
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   }
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   else  hstepm=estepm;
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+    * This is mainly to measure the difference between two models: for example
-     gp=matrix(0,nhstepm,1,nlstate);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     gm=matrix(0,nhstepm,1,nlstate);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-     for(theta=1; theta <=npar; theta++){
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+    * to compare the new estimate of Life expectancy with the same linear
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+    * hypothesis. A more precise result, taking into account a more precise
-       }
+    * curvature will be obtained if estepm is as small as stepm. */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       if (popbased==1) {
+      nhstepm is the number of hstepm from age to agelim
-         if(mobilav ==0){
+      nstepm is the number of stepm from age to agelin.
-           for(i=1; i<=nlstate;i++)
+      Look at hpijx to understand the reason of that which relies in memory size
-             prlim[i][i]=probs[(int)age][i][ij];
+      and note for a fixed period like estepm months */
-         }else{ /* mobilav */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-           for(i=1; i<=nlstate;i++)
+      survival function given by stepm (the optimization length). Unfortunately it
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+      means that if the survival funtion is printed only each two years of age and if
-         }
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-       }
+      results. So we changed our mind and took the option of the best precision.
+   */
-       for(j=1; j<= nlstate; j++){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+   agelim=AGESUP;
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+   /* If stepm=6 months */
-         }
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-       }
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+ /* nhstepm age range expressed in number of stepm */
-          as a weighted average of prlim.
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   /* if (stepm >= YEARM) hstepm=1;*/
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
-       /* end probability of death */
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     /* if (stepm >= YEARM) hstepm=1;*/
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     /* If stepm=6 months */
-       if (popbased==1) {
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-         if(mobilav ==0){
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+     printf("%d|",(int)age);fflush(stdout);
-       }
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       for(j=1; j<= nlstate; j++){
+     /* Computing expectancies */
-         for(h=0; h<=nhstepm; h++){
+     for(i=1; i<=nlstate;i++)
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-         }
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       }
-       /* This for computing probability of death (h=1 means
+           /* 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]);*/
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+         }
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+     fprintf(ficreseij,"%3.0f",age );
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+     for(i=1; i<=nlstate;i++){
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       eip=0;
-       }
+       for(j=1; j<=nlstate;j++){
-       /* end probability of death */
+         eip +=eij[i][j][(int)age];
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-       for(j=1; j<= nlstate; j++) /* vareij */
+       }
-         for(h=0; h<=nhstepm; h++){
+       fprintf(ficreseij,"%9.4f", eip );
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+     }
-         }
+     fprintf(ficreseij,"\n");
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   }
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
+   printf("\n");
+   fprintf(ficlog,"\n");
-     } /* End theta */
+ }
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+ 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[] )
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
+ {
-         for(theta=1; theta <=npar; theta++)
+   /* Covariances of health expectancies eij and of total life expectancies according
-           trgradg[h][j][theta]=gradg[h][theta][j];
+    to initial status i, ei. .
+   */
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-       for(theta=1; theta <=npar; theta++)
+   int nhstepma, nstepma; /* Decreasing with age */
-         trgradgp[j][theta]=gradgp[theta][j];
+   double age, agelim, hf;
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   double *xp, *xm;
-     for(i=1;i<=nlstate;i++)
+   double **gp, **gm;
-       for(j=1;j<=nlstate;j++)
+   double ***gradg, ***trgradg;
-         vareij[i][j][(int)age] =0.;
+   int theta;
-     for(h=0;h<=nhstepm;h++){
+   double eip, vip;
-       for(k=0;k<=nhstepm;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+   xp=vector(1,npar);
-         for(i=1;i<=nlstate;i++)
+   xm=vector(1,npar);
-           for(j=1;j<=nlstate;j++)
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-       }
-     }
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     /* pptj */
+   fprintf(ficresstdeij,"# Age");
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   for(i=1; i<=nlstate;i++){
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+     for(j=1; j<=nlstate;j++)
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+     fprintf(ficresstdeij," e%1d. ",i);
-         varppt[j][i]=doldmp[j][i];
+   }
-     /* end ppptj */
+   fprintf(ficresstdeij,"\n");
-     /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   pstamp(ficrescveij);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   fprintf(ficrescveij,"# Age");
-     if (popbased==1) {
+   for(i=1; i<=nlstate;i++)
-       if(mobilav ==0){
+     for(j=1; j<=nlstate;j++){
-         for(i=1; i<=nlstate;i++)
+       cptj= (j-1)*nlstate+i;
-           prlim[i][i]=probs[(int)age][i][ij];
+       for(i2=1; i2<=nlstate;i2++)
-       }else{ /* mobilav */
+         for(j2=1; j2<=nlstate;j2++){
-         for(i=1; i<=nlstate;i++)
+           cptj2= (j2-1)*nlstate+i2;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+           if(cptj2 <= cptj)
-       }
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-     }
+         }
+     }
-     /* This for computing probability of death (h=1 means
+   fprintf(ficrescveij,"\n");
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
+   if(estepm < stepm){
-     */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   }
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   else  hstepm=estepm;
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     }
+    * This is mainly to measure the difference between two models: for example
-     /* end probability of death */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+    * progression in between and thus overestimating or underestimating according
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+    * to the curvature of the survival function. If, for the same date, we
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-       for(i=1; i<=nlstate;i++){
+    * to compare the new estimate of Life expectancy with the same linear
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+    * hypothesis. A more precise result, taking into account a more precise
-       }
+    * curvature will be obtained if estepm is as small as stepm. */
-     }
-     fprintf(ficresprobmorprev,"\n");
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     fprintf(ficresvij,"%.0f ",age );
+      nhstepm is the number of hstepm from age to agelim
-     for(i=1; i<=nlstate;i++)
+      nstepm is the number of stepm from age to agelin.
-       for(j=1; j<=nlstate;j++){
+      Look at hpijx to understand the reason of that which relies in memory size
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+      and note for a fixed period like estepm months */
-       }
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     fprintf(ficresvij,"\n");
+      survival function given by stepm (the optimization length). Unfortunately it
-     free_matrix(gp,0,nhstepm,1,nlstate);
+      means that if the survival funtion is printed only each two years of age and if
-     free_matrix(gm,0,nhstepm,1,nlstate);
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+      results. So we changed our mind and took the option of the best precision.
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   */
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+   /* If stepm=6 months */
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   /* nhstepm age range expressed in number of stepm */
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   agelim=AGESUP;
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- /*   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); */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   for (age=bage; age<=fage; age ++){
- */
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+     /* If stepm=6 months */
-   free_matrix(dnewm,1,nlstate,1,npar);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
+     /* Computing  Variances of health expectancies */
-   fflush(ficgp);
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   fflush(fichtm);
+        decrease memory allocation */
- }  /* end varevsij */
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){
- /************ Variance of prevlim ******************/
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
- {
+       }
-   /* Variance of prevalence limit */
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   double **newm;
-   double **dnewm,**doldm;
+       for(j=1; j<= nlstate; j++){
-   int i, j, nhstepm, hstepm;
+         for(i=1; i<=nlstate; i++){
-   int k, cptcode;
+           for(h=0; h<=nhstepm-1; h++){
-   double *xp;
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   double *gp, *gm;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   double **gradg, **trgradg;
+           }
-   double age,agelim;
+         }
-   int theta;
+       }
-   pstamp(ficresvpl);
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+         for(h=0; h<=nhstepm-1; h++){
-   fprintf(ficresvpl,"# Age");
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   for(i=1; i<=nlstate;i++)
+         }
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     }/* End theta */
-   fprintf(ficresvpl,"\n");
-   xp=vector(1,npar);
+     for(h=0; h<=nhstepm-1; h++)
-   dnewm=matrix(1,nlstate,1,npar);
+       for(j=1; j<=nlstate*nlstate;j++)
-   doldm=matrix(1,nlstate,1,nlstate);
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   hstepm=1*YEARM; /* Every year of age */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         varhe[ij][ji][(int)age] =0.;
-     if (stepm >= YEARM) hstepm=1;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+      printf("%d|",(int)age);fflush(stdout);
-     gradg=matrix(1,npar,1,nlstate);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-     gp=vector(1,nlstate);
+      for(h=0;h<=nhstepm-1;h++){
-     gm=vector(1,nlstate);
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-     for(theta=1; theta <=npar; theta++){
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-       }
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       for(i=1;i<=nlstate;i++)
+     }
-         gp[i] = prlim[i][i];
+     /* Computing expectancies */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     for(i=1; i<=nlstate;i++)
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       for(j=1; j<=nlstate;j++)
-       for(i=1;i<=nlstate;i++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-         gm[i] = prlim[i][i];
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-       for(i=1;i<=nlstate;i++)
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-     } /* End theta */
+         }
-     trgradg =matrix(1,nlstate,1,npar);
+     fprintf(ficresstdeij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-     for(j=1; j<=nlstate;j++)
+       eip=0.;
-       for(theta=1; theta <=npar; theta++)
+       vip=0.;
-         trgradg[j][theta]=gradg[theta][j];
+       for(j=1; j<=nlstate;j++){
+         eip += eij[i][j][(int)age];
-     for(i=1;i<=nlstate;i++)
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-       varpl[i][(int)age] =0.;
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+       }
-     for(i=1;i<=nlstate;i++)
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     }
+     fprintf(ficresstdeij,"\n");
-     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+     fprintf(ficrescveij,"%3.0f",age );
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+     for(i=1; i<=nlstate;i++)
-     fprintf(ficresvpl,"\n");
+       for(j=1; j<=nlstate;j++){
-     free_vector(gp,1,nlstate);
+         cptj= (j-1)*nlstate+i;
-     free_vector(gm,1,nlstate);
+         for(i2=1; i2<=nlstate;i2++)
-     free_matrix(gradg,1,npar,1,nlstate);
+           for(j2=1; j2<=nlstate;j2++){
-     free_matrix(trgradg,1,nlstate,1,npar);
+             cptj2= (j2-1)*nlstate+i2;
-   } /* End age */
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-   free_vector(xp,1,npar);
+           }
-   free_matrix(doldm,1,nlstate,1,npar);
+       }
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+     fprintf(ficrescveij,"\n");
- }
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
- /************ Variance of one-step probabilities  ******************/
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- 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[])
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
- {
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   int i, j=0,  i1, k1, l1, t, tj;
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int k2, l2, j1,  z1;
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int k=0,l, cptcode;
+   printf("\n");
-   int first=1, first1;
+   fprintf(ficlog,"\n");
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+   free_vector(xm,1,npar);
-   double *xp;
+   free_vector(xp,1,npar);
-   double *gp, *gm;
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   double **gradg, **trgradg;
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   double **mu;
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-   double age,agelim, cov[NCOVMAX];
+ }
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+ /************ Variance ******************/
-   char fileresprob[FILENAMELENGTH];
+ 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[])
-   char fileresprobcov[FILENAMELENGTH];
+ {
-   char fileresprobcor[FILENAMELENGTH];
+   /* Variance of health expectancies */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   double ***varpij;
+   /* double **newm;*/
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-   strcpy(fileresprob,"prob");
-   strcat(fileresprob,fileres);
+   int movingaverage();
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   double **dnewm,**doldm;
-     printf("Problem with resultfile: %s\n", fileresprob);
+   double **dnewmp,**doldmp;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   }
+   int k;
-   strcpy(fileresprobcov,"probcov");
+   double *xp;
-   strcat(fileresprobcov,fileres);
+   double **gp, **gm;  /* for var eij */
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   double ***gradg, ***trgradg; /*for var eij */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   double **gradgp, **trgradgp; /* for var p point j */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   double *gpp, *gmp; /* for var p point j */
-   }
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   strcpy(fileresprobcor,"probcor");
+   double ***p3mat;
-   strcat(fileresprobcor,fileres);
+   double age,agelim, hf;
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   double ***mobaverage;
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+   int theta;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   char digit[4];
-   }
+   char digitp[25];
-   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);
+   char fileresprobmorprev[FILENAMELENGTH];
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   if(popbased==1){
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+     if(mobilav!=0)
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+       strcpy(digitp,"-populbased-mobilav-");
-   pstamp(ficresprob);
+     else strcpy(digitp,"-populbased-nomobil-");
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   }
-   fprintf(ficresprob,"# Age");
+   else
-   pstamp(ficresprobcov);
+     strcpy(digitp,"-stablbased-");
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   if (mobilav!=0) {
-   pstamp(ficresprobcor);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   fprintf(ficresprobcor,"# Age");
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
-   for(i=1; i<=nlstate;i++)
+   }
-     for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   strcpy(fileresprobmorprev,"prmorprev");
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   sprintf(digit,"%-d",ij);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-     }
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-  /* fprintf(ficresprob,"\n");
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   fprintf(ficresprobcov,"\n");
+   strcat(fileresprobmorprev,fileres);
-   fprintf(ficresprobcor,"\n");
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-  */
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-  xp=vector(1,npar);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   }
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   first=1;
+   pstamp(ficresprobmorprev);
-   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   fprintf(fichtm,"\n");
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   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\
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   file %s<br>\n",optionfilehtmcov);
+   }
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   fprintf(ficresprobmorprev,"\n");
- and drawn. It helps understanding how is the covariance between two incidences.\
+   fprintf(ficgp,"\n# Routine varevsij");
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   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(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");
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ /*   } */
- standard deviations wide on each axis. <br>\
+   varppt = 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\
+   pstamp(ficresvij);
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+   if(popbased==1)
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   cov[1]=1;
+   else
-   tj=cptcoveff;
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   fprintf(ficresvij,"# Age");
-   j1=0;
+   for(i=1; i<=nlstate;i++)
-   for(t=1; t<=tj;t++){
+     for(j=1; j<=nlstate;j++)
-     for(i1=1; i1<=ncodemax[t];i1++){
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-       j1++;
+   fprintf(ficresvij,"\n");
-       if  (cptcovn>0) {
-         fprintf(ficresprob, "\n#********** Variable ");
+   xp=vector(1,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   dnewm=matrix(1,nlstate,1,npar);
-         fprintf(ficresprob, "**********\n#\n");
+   doldm=matrix(1,nlstate,1,nlstate);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         fprintf(ficresprobcov, "**********\n#\n");
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-         fprintf(ficgp, "\n#********** Variable ");
+   gpp=vector(nlstate+1,nlstate+ndeath);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-         fprintf(ficgp, "**********\n#\n");
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   if(estepm < stepm){
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   }
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   else  hstepm=estepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      nhstepm is the number of hstepm from age to agelim
-         fprintf(ficresprobcor, "**********\n#");
+      nstepm is the number of stepm from age to agelin.
-       }
+      Look at function hpijx to understand why (it is linked to memory size questions) */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       for (age=bage; age<=fage; age ++){
+      survival function given by stepm (the optimization length). Unfortunately it
-         cov[2]=age;
+      means that if the survival funtion is printed every two years of age and if
-         for (k=1; k<=cptcovn;k++) {
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+      results. So we changed our mind and took the option of the best precision.
-         }
+   */
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for (k=1; k<=cptcovprod;k++)
+   agelim = AGESUP;
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+     gp=matrix(0,nhstepm,1,nlstate);
+     gm=matrix(0,nhstepm,1,nlstate);
-         for(theta=1; theta <=npar; theta++){
-           for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
-           k=0;
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-           for(i=1; i<= (nlstate); i++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+       if (popbased==1) {
-               gp[k]=pmmij[i][j];
+         if(mobilav ==0){
-             }
+           for(i=1; i<=nlstate;i++)
-           }
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
-           for(i=1; i<=npar; i++)
+           for(i=1; i<=nlstate;i++)
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+       }
-           k=0;
-           for(i=1; i<=(nlstate); i++){
+       for(j=1; j<= nlstate; j++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+         for(h=0; h<=nhstepm; h++){
-               k=k+1;
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-               gm[k]=pmmij[i][j];
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-             }
+         }
-           }
+       }
+       /* This for computing probability of death (h=1 means
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+          computed over hstepm matrices product = hstepm*stepm months)
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+          as a weighted average of prlim.
-         }
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           for(theta=1; theta <=npar; theta++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-             trgradg[j][theta]=gradg[theta][j];
+       }
+       /* end probability of death */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       if (popbased==1) {
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-         k=0;
+             prlim[i][i]=probs[(int)age][i][ij];
-         for(i=1; i<=(nlstate); i++){
+         }else{ /* mobilav */
-           for(j=1; j<=(nlstate+ndeath);j++){
+           for(i=1; i<=nlstate;i++)
-             k=k+1;
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-             mu[k][(int) age]=pmmij[i][j];
+         }
-           }
+       }
-         }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+         for(h=0; h<=nhstepm; h++){
-             varpij[i][j][(int)age] = doldm[i][j];
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         /*printf("\n%d ",(int)age);
+         }
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+       }
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+       /* This for computing probability of death (h=1 means
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          computed over hstepm matrices product = hstepm*stepm months)
-           }*/
+          as a weighted average of prlim.
+       */
-         fprintf(ficresprob,"\n%d ",(int)age);
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+       /* end probability of death */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+       for(j=1; j<= nlstate; j++) /* vareij */
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+         for(h=0; h<=nhstepm; h++){
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }
-         i=0;
-         for (k=1; k<=(nlstate);k++){
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-           for (l=1; l<=(nlstate+ndeath);l++){
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-             i=i++;
+       }
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     } /* End theta */
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
+     for(h=0; h<=nhstepm; h++) /* veij */
-           }
+       for(j=1; j<=nlstate;j++)
-         }/* end of loop for state */
+         for(theta=1; theta <=npar; theta++)
-       } /* end of loop for age */
+           trgradg[h][j][theta]=gradg[h][theta][j];
-       /* Confidence intervalle of pij  */
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       /*
+       for(theta=1; theta <=npar; theta++)
-         fprintf(ficgp,"\nset noparametric;unset label");
+         trgradgp[j][theta]=gradgp[theta][j];
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+     for(i=1;i<=nlstate;i++)
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+       for(j=1;j<=nlstate;j++)
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+         vareij[i][j][(int)age] =0.;
-       */
+     for(h=0;h<=nhstepm;h++){
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       for(k=0;k<=nhstepm;k++){
-       first1=1;
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-       for (k2=1; k2<=(nlstate);k2++){
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+         for(i=1;i<=nlstate;i++)
-           if(l2==k2) continue;
+           for(j=1;j<=nlstate;j++)
-           j=(k2-1)*(nlstate+ndeath)+l2;
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-           for (k1=1; k1<=(nlstate);k1++){
+       }
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+     }
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+     /* pptj */
-               if(i<=j) continue;
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-               for (age=bage; age<=fage; age ++){
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-                 if ((int)age %5==0){
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+         varppt[j][i]=doldmp[j][i];
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     /* end ppptj */
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+     /*  x centered again */
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-                   c12=cv12/sqrt(v1*v2);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-                   /* Computing eigen value of matrix of covariance */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     if (popbased==1) {
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       if(mobilav ==0){
-                   /* Eigen vectors */
+         for(i=1; i<=nlstate;i++)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+           prlim[i][i]=probs[(int)age][i][ij];
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+       }else{ /* mobilav */
-                   v21=(lc1-v1)/cv12*v11;
+         for(i=1; i<=nlstate;i++)
-                   v12=-v21;
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-                   v22=v11;
+       }
-                   tnalp=v21/v11;
+     }
-                   if(first1==1){
-                     first1=0;
+     /* This for computing probability of death (h=1 means
-                     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);
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-                   }
+        as a weighted average of prlim.
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+     */
-                   /*printf(fignu*/
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-                   if(first==1){
+     }
-                     first=0;
+     /* end probability of death */
-                     fprintf(ficgp,"\nset parametric;unset label");
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+       for(i=1; i<=nlstate;i++){
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+       }
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+     }
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+     fprintf(ficresprobmorprev,"\n");
-                     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(ficresvij,"%.0f ",age );
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+     for(i=1; i<=nlstate;i++)
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+       for(j=1; j<=nlstate;j++){
-                     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(ficresvij," %.4f", vareij[i][j][(int)age]);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       }
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+     fprintf(ficresvij,"\n");
-                   }else{
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                     first=0;
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+   } /* End age */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                   }/* if first */
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                 } /* age mod 5 */
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-               } /* end loop age */
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-               first=1;
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-             } /*l12 */
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-           } /* k12 */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         } /*l1 */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-       }/* k1 */
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-     } /* loop covariates */
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-   }
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   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);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   /*  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);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+ */
-   free_vector(xp,1,npar);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fclose(ficresprob);
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   fclose(ficresprobcov);
-   fclose(ficresprobcor);
+   free_vector(xp,1,npar);
-   fflush(ficgp);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-   fflush(fichtmcov);
+   free_matrix(dnewm,1,nlstate,1,npar);
- }
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- /******************* Printing html file ***********/
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   fclose(ficresprobmorprev);
-                   int lastpass, int stepm, int weightopt, char model[],\
+   fflush(ficgp);
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   fflush(fichtm);
-                   int popforecast, int estepm ,\
+ }  /* end varevsij */
-                   double jprev1, double mprev1,double anprev1, \
-                   double jprev2, double mprev2,double anprev2){
+ /************ Variance of prevlim ******************/
-   int jj1, k1, i1, cpt;
+ 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[])
+ {
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   /* Variance of prevalence limit */
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- </ul>");
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   double **dnewm,**doldm;
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+   int i, j, nhstepm, hstepm;
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   double *xp;
-    fprintf(fichtm,"\
+   double *gp, *gm;
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   double **gradg, **trgradg;
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   double age,agelim;
-    fprintf(fichtm,"\
+   int theta;
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   pstamp(ficresvpl);
-    fprintf(fichtm,"\
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-  - (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): \
+   fprintf(ficresvpl,"# Age");
-    <a href=\"%s\">%s</a> <br>\n",
+   for(i=1; i<=nlstate;i++)
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+       fprintf(ficresvpl," %1d-%1d",i,i);
-    fprintf(fichtm,"\
+   fprintf(ficresvpl,"\n");
-  - Population projections by age and states: \
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+   xp=vector(1,npar);
+   dnewm=matrix(1,nlstate,1,npar);
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+   doldm=matrix(1,nlstate,1,nlstate);
-  m=cptcoveff;
+   hstepm=1*YEARM; /* Every year of age */
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGESUP;
-  jj1=0;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-  for(k1=1; k1<=m;k1++){
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     if (stepm >= YEARM) hstepm=1;
-      jj1++;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-      if (cptcovn > 0) {
+     gradg=matrix(1,npar,1,nlstate);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     gp=vector(1,nlstate);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+     gm=vector(1,nlstate);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     for(theta=1; theta <=npar; theta++){
-      }
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-      /* Pij */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-      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> \
+       }
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-      /* Quasi-incidences */
+       for(i=1;i<=nlstate;i++)
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+         gp[i] = prlim[i][i];
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       for(i=1; i<=npar; i++) /* Computes gradient */
-        /* Period (stable) prevalence in each health state */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-        for(cpt=1; cpt<nlstate;cpt++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-          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);
+         gm[i] = prlim[i][i];
-        }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+       for(i=1;i<=nlstate;i++)
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+     } /* End theta */
-      }
-    } /* end i1 */
+     trgradg =matrix(1,nlstate,1,npar);
-  }/* End k1 */
-  fprintf(fichtm,"</ul>");
+     for(j=1; j<=nlstate;j++)
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
-  fprintf(fichtm,"\
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+     for(i=1;i<=nlstate;i++)
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+       varpl[i][(int)age] =0.;
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+     for(i=1;i<=nlstate;i++)
-  fprintf(fichtm,"\
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+     fprintf(ficresvpl,"%.0f ",age );
+     for(i=1; i<=nlstate;i++)
-  fprintf(fichtm,"\
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+     fprintf(ficresvpl,"\n");
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+     free_vector(gp,1,nlstate);
-  fprintf(fichtm,"\
+     free_vector(gm,1,nlstate);
-  - 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): \
+     free_matrix(gradg,1,npar,1,nlstate);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+     free_matrix(trgradg,1,nlstate,1,npar);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   } /* End age */
-  fprintf(fichtm,"\
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+   free_vector(xp,1,npar);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   free_matrix(doldm,1,nlstate,1,npar);
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-  fprintf(fichtm,"\
-  - 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",
+ }
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-  fprintf(fichtm,"\
+ /************ Variance of one-step probabilities  ******************/
-  - 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",
+ 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[])
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ {
-  fprintf(fichtm,"\
+   int i, j=0,  k1, l1, tj;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   int k2, l2, j1,  z1;
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   int k=0, l;
+   int first=1, first1, first2;
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   double **dnewm,**doldm;
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   double *xp;
- /*      <br>",fileres,fileres,fileres,fileres); */
+   double *gp, *gm;
- /*  else  */
+   double **gradg, **trgradg;
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+   double **mu;
-  fflush(fichtm);
+   double age, cov[NCOVMAX+1];
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   int theta;
-  m=cptcoveff;
+   char fileresprob[FILENAMELENGTH];
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
-  jj1=0;
+   double ***varpij;
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   strcpy(fileresprob,"prob");
-      jj1++;
+   strcat(fileresprob,fileres);
-      if (cptcovn > 0) {
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     printf("Problem with resultfile: %s\n", fileresprob);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   }
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   strcpy(fileresprobcov,"probcov");
-      }
+   strcat(fileresprobcov,fileres);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+     printf("Problem with resultfile: %s\n", fileresprobcov);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   }
-      }
+   strcpy(fileresprobcor,"probcor");
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   strcat(fileresprobcor,fileres);
- health expectancies in states (1) and (2): %s%d.png<br>\
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-    } /* end i1 */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-  }/* End k1 */
+   }
-  fprintf(fichtm,"</ul>");
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-  fflush(fichtm);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- }
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- /******************* Gnuplot file **************/
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
-   char dirfileres[132],optfileres[132];
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   fprintf(ficresprob,"# Age");
-   int ng;
+   pstamp(ficresprobcov);
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- /*     printf("Problem with file %s",optionfilegnuplot); */
+   fprintf(ficresprobcov,"# Age");
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   pstamp(ficresprobcor);
- /*   } */
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcor,"# Age");
-   /*#ifdef windows */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   for(i=1; i<=nlstate;i++)
-   m=pow(2,cptcoveff);
+     for(j=1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-   strcpy(dirfileres,optionfilefiname);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-   strcpy(optfileres,"vpl");
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-  /* 1eme*/
+     }
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+  /* fprintf(ficresprob,"\n");
-    for (k1=1; k1<= m ; k1 ++) {
+   fprintf(ficresprobcov,"\n");
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   fprintf(ficresprobcor,"\n");
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+  */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+   xp=vector(1,npar);
- set ylabel \"Probability\" \n\
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- set ter png small\n\
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- set size 0.65,0.65\n\
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
-      for (i=1; i<= nlstate ; i ++) {
+   fprintf(ficgp,"\n# Routine varprob");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   fprintf(fichtm,"\n");
-      }
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+   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\
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   file %s<br>\n",optionfilehtmcov);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-      }
+ and drawn. It helps understanding how is the covariance between two incidences.\
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-      for (i=1; i<= nlstate ; i ++) {
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-      }
+ standard deviations wide on each axis. <br>\
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-    }
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-   }
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   /*2 eme*/
+   cov[1]=1;
-   for (k1=1; k1<= m ; k1 ++) {
+   /* tj=cptcoveff; */
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+   tj = (int) pow(2,cptcoveff);
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   j1=0;
-     for (i=1; i<= nlstate+1 ; i ++) {
+   for(j1=1; j1<=tj;j1++){
-       k=2*i;
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     /*j1++;*/
-       for (j=1; j<= nlstate+1 ; j ++) {
+       if  (cptcovn>0) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficresprob, "\n#********** Variable ");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       }
+         fprintf(ficresprob, "**********\n#\n");
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+         fprintf(ficresprobcov, "\n#********** Variable ");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         fprintf(ficresprobcov, "**********\n#\n");
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp, "\n#********** Variable ");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       }
+         fprintf(ficgp, "**********\n#\n");
-       fprintf(ficgp,"\" t\"\" w l 0,");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-       }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+         fprintf(ficresprobcor, "\n#********** Variable ");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-     }
+         fprintf(ficresprobcor, "**********\n#");
-   }
+       }
-   /*3eme*/
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   for (k1=1; k1<= m ; k1 ++) {
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-       /*       k=2+nlstate*(2*cpt-2); */
+       for (age=bage; age<=fage; age ++){
-       k=2+(nlstate+1)*(cpt-1);
+         cov[2]=age;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+         for (k=1; k<=cptcovn;k++) {
-       fprintf(ficgp,"set ter png small\n\
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
- set size 0.65,0.65\n\
+                                                          * 1  1 1 1 1
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+                                                          * 2  2 1 1 1
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                                                          * 3  1 2 1 1
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                                          */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         }
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       */
-       for (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);
+         for(theta=1; theta <=npar; theta++){
-         /*      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);*/
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-     }
-   }
+           k=0;
+           for(i=1; i<= (nlstate); i++){
-   /* CV preval stable (period) */
+             for(j=1; j<=(nlstate+ndeath);j++){
-   for (k1=1; k1<= m ; k1 ++) {
+               k=k+1;
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+               gp[k]=pmmij[i][j];
-       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\
- set ter png small\nset size 0.65,0.65\n\
+           for(i=1; i<=npar; i++)
- unset log y\n\
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       for (i=1; i< nlstate ; i ++)
+           k=0;
-         fprintf(ficgp,"+$%d",k+i+1);
+           for(i=1; i<=(nlstate); i++){
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
-       l=3+(nlstate+ndeath)*cpt;
+               gm[k]=pmmij[i][j];
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+             }
-       for (i=1; i< nlstate ; i ++) {
+           }
-         l=3+(nlstate+ndeath)*cpt;
-         fprintf(ficgp,"+$%d",l+i+1);
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-       }
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+         }
-     }
-   }
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+           for(theta=1; theta <=npar; theta++)
-   /* proba elementaires */
+             trgradg[j][theta]=gradg[theta][j];
-   for(i=1,jk=1; i <=nlstate; i++){
-     for(k=1; k <=(nlstate+ndeath); k++){
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       if (k != i) {
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         for(j=1; j <=ncovmodel; j++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-           jk++;
-           fprintf(ficgp,"\n");
+         k=0;
-         }
+         for(i=1; i<=(nlstate); i++){
-       }
+           for(j=1; j<=(nlstate+ndeath);j++){
-     }
+             k=k+1;
-    }
+             mu[k][(int) age]=pmmij[i][j];
+           }
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+         }
-      for(jk=1; jk <=m; jk++) {
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-        if (ng==2)
+             varpij[i][j][(int)age] = doldm[i][j];
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-        else
+         /*printf("\n%d ",(int)age);
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-        i=1;
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-        for(k2=1; k2<=nlstate; k2++) {
+           }*/
-          k3=i;
-          for(k=1; k<=(nlstate+ndeath); k++) {
+         fprintf(ficresprob,"\n%d ",(int)age);
-            if (k != k2){
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-              if(ng==2)
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-              else
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-              ij=1;
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-              for(j=3; j <=ncovmodel; j++) {
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         }
-                  ij++;
+         i=0;
-                }
+         for (k=1; k<=(nlstate);k++){
-                else
+           for (l=1; l<=(nlstate+ndeath);l++){
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+             i++;
-              }
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-              fprintf(ficgp,")/(1");
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+             for (j=1; j<=i;j++){
-              for(k1=1; k1 <=nlstate; k1++){
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-                ij=1;
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-                for(j=3; j <=ncovmodel; j++){
+             }
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+           }
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         }/* end of loop for state */
-                    ij++;
+       } /* end of loop for age */
-                  }
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-                  else
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                }
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                fprintf(ficgp,")");
-              }
+       /* Confidence intervalle of pij  */
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       /*
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+         fprintf(ficgp,"\nunset parametric;unset label");
-              i=i+ncovmodel;
+         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");
-          } /* end k */
+         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);
-        } /* end k2 */
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-      } /* end jk */
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-    } /* end ng */
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-    fflush(ficgp);
+       */
- }  /* end gnuplot */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;first2=2;
- /*************** Moving average **************/
+       for (k2=1; k2<=(nlstate);k2++){
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
-   int i, cpt, cptcod;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-   int modcovmax =1;
+           for (k1=1; k1<=(nlstate);k1++){
-   int mobilavrange, mob;
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-   double age;
+               if(l1==k1) continue;
+               i=(k1-1)*(nlstate+ndeath)+l1;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+               if(i<=j) continue;
-                            a covariate has 2 modalities */
+               for (age=bage; age<=fage; age ++){
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-     if(mobilav==1) mobilavrange=5; /* default */
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-     else mobilavrange=mobilav;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-     for (age=bage; age<=fage; age++)
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-       for (i=1; i<=nlstate;i++)
+                   c12=cv12/sqrt(v1*v2);
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                   /* Computing eigen value of matrix of covariance */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     /* We keep the original values on the extreme ages bage, fage and for
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                   if ((lc2 <0) || (lc1 <0) ){
-        we use a 5 terms etc. until the borders are no more concerned.
+                     if(first2==1){
-     */
+                       first1=0;
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                     }
-         for (i=1; i<=nlstate;i++){
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                     /* lc2=fabs(lc2); */
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                   }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                   /* Eigen vectors */
-               }
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-           }
+                   v21=(lc1-v1)/cv12*v11;
-         }
+                   v12=-v21;
-       }/* end age */
+                   v22=v11;
-     }/* end mob */
+                   tnalp=v21/v11;
-   }else return -1;
+                   if(first1==1){
-   return 0;
+                     first1=0;
- }/* End movingaverage */
+                     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(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);
- /************** Forecasting ******************/
+                   /*printf(fignu*/
- 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){
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-   /* proj1, year, month, day of starting projection
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-      agemin, agemax range of age
+                   if(first==1){
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+                     first=0;
-      anproj2 year of en of projection (same day and month as proj1).
+                     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);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-   int *popage;
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-   double agec; /* generic age */
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-   double *popeffectif,*popcount;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-   double ***p3mat;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   double ***mobaverage;
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   char fileresf[FILENAMELENGTH];
+                     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);
-   agelim=AGESUP;
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-   strcpy(fileresf,"f");
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   strcat(fileresf,fileres);
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+                   }else{
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+                     first=0;
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-   }
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
-   if (mobilav!=0) {
+                 } /* age mod 5 */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+               } /* end loop age */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+               first=1;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+             } /*l12 */
-     }
+           } /* k12 */
-   }
+         } /*l1 */
+       }/* k1 */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+       /* } */ /* loop covariates */
-   if (stepm<=12) stepsize=1;
+   }
-   if(estepm < stepm){
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   }
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   else  hstepm=estepm;
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   free_vector(xp,1,npar);
-   hstepm=hstepm/stepm;
+   fclose(ficresprob);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+   fclose(ficresprobcov);
-                                fractional in yp1 */
+   fclose(ficresprobcor);
-   anprojmean=yp;
+   fflush(ficgp);
-   yp2=modf((yp1*12),&yp);
+   fflush(fichtmcov);
-   mprojmean=yp;
+ }
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
-   if(jprojmean==0) jprojmean=1;
+ /******************* Printing html file ***********/
-   if(mprojmean==0) jprojmean=1;
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
-   i1=cptcoveff;
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   if (cptcovn < 1){i1=1;}
+                   int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
- /*            if (h==(int)(YEARM*yearp)){ */
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+ </ul>");
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-       k=k+1;
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-       fprintf(ficresf,"\n#******");
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-       for(j=1;j<=cptcoveff;j++) {
+    fprintf(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]]);
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-       }
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-       fprintf(ficresf,"******\n");
+    fprintf(fichtm,"\
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-       for(j=1; j<=nlstate+ndeath;j++){
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-         for(i=1; i<=nlstate;i++)
+    fprintf(fichtm,"\
-           fprintf(ficresf," p%d%d",i,j);
+  - (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," p.%d",j);
+    <a href=\"%s\">%s</a> <br>\n",
-       }
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+    fprintf(fichtm,"\
-         fprintf(ficresf,"\n");
+  - Population projections by age and states: \
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
+  m=pow(2,cptcoveff);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
-           for (h=0; h<=nhstepm; h++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
-             if (h*hstepm/YEARM*stepm ==yearp) {
+      jj1++;
-               fprintf(ficresf,"\n");
+      if (cptcovn > 0) {
-               for(j=1;j<=cptcoveff;j++)
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-             }
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-             for(j=1; j<=nlstate+ndeath;j++) {
+      }
-               ppij=0.;
+      /* Pij */
-               for(i=1; i<=nlstate;i++) {
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-                 if (mobilav==1)
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+      /* Quasi-incidences */
-                 else {
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-                 }
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                 if (h*hstepm/YEARM*stepm== yearp) {
+        /* Period (stable) prevalence in each health state */
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+        for(cpt=1; cpt<=nlstate;cpt++){
-                 }
+          fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
-               } /* end i */
+ <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-               if (h*hstepm/YEARM*stepm==yearp) {
+        }
-                 fprintf(ficresf," %.3f", ppij);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-               }
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-             }/* end j */
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-           } /* end h */
+      }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    } /* end i1 */
-         } /* end agec */
+  }/* End k1 */
-       } /* end yearp */
+  fprintf(fichtm,"</ul>");
-     } /* end cptcod */
-   } /* end  cptcov */
+  fprintf(fichtm,"\
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ \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);
-   fclose(ficresf);
- }
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
- /************** Forecasting *****not tested NB*************/
+  fprintf(fichtm,"\
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   int *popage;
+  fprintf(fichtm,"\
-   double calagedatem, agelim, kk1, kk2;
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-   double *popeffectif,*popcount;
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-   double ***p3mat,***tabpop,***tabpopprev;
+  fprintf(fichtm,"\
-   double ***mobaverage;
+  - 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): \
-   char filerespop[FILENAMELENGTH];
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  fprintf(fichtm,"\
-   tabpopprev= ma3x(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): \
-   agelim=AGESUP;
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
-   strcpy(filerespop,"pop");
+  - 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",
-   strcat(filerespop,fileres);
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+  fprintf(fichtm,"\
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ /*  - 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 */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*      <br>",fileres,fileres,fileres,fileres); */
+ /*  else  */
-   if (mobilav!=0) {
+ /*    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); */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  fflush(fichtm);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+  m=pow(2,cptcoveff);
-     }
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   }
+  jj1=0;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+  for(k1=1; k1<=m;k1++){
-   if (stepm<=12) stepsize=1;
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
-   agelim=AGESUP;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   hstepm=1;
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   hstepm=hstepm/stepm;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   if (popforecast==1) {
+      }
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-       printf("Problem with population file : %s\n",popfile);exit(0);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-     }
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-     popage=ivector(0,AGESUP);
+      }
-     popeffectif=vector(0,AGESUP);
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-     popcount=vector(0,AGESUP);
+ 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\
-     i=1;
+  drawn in addition to the population based expectancies computed using\
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-     imx=i;
+    } /* end i1 */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+  }/* End k1 */
-   }
+  fprintf(fichtm,"</ul>");
+  fflush(fichtm);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ }
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       k=k+1;
+ /******************* Gnuplot file **************/
-       fprintf(ficrespop,"\n#******");
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   char dirfileres[132],optfileres[132];
-       }
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-       fprintf(ficrespop,"******\n");
+   int ng=0;
-       fprintf(ficrespop,"# Age");
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+ /*   } */
-       for (cpt=0; cpt<=0;cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     /*#endif */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   m=pow(2,cptcoveff);
-           nhstepm = nhstepm/hstepm;
+   strcpy(dirfileres,optionfilefiname);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   strcpy(optfileres,"vpl");
-           oldm=oldms;savm=savms;
+  /* 1eme*/
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-           for (h=0; h<=nhstepm; h++){
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-             }
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-             for(j=1; j<=nlstate+ndeath;j++) {
+ set ylabel \"Probability\" \n\
-               kk1=0.;kk2=0;
+ set ter png small size 320, 240\n\
-               for(i=1; i<=nlstate;i++) {
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-                 if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+      for (i=1; i<= nlstate ; i ++) {
-                 else {
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+        else        fprintf(ficgp," %%*lf (%%*lf)");
-                 }
+      }
-               }
+      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);
-               if (h==(int)(calagedatem+12*cpt)){
+      for (i=1; i<= nlstate ; i ++) {
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-                   /*fprintf(ficrespop," %.3f", kk1);
+        else fprintf(ficgp," %%*lf (%%*lf)");
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+      }
-               }
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-             }
+      for (i=1; i<= nlstate ; i ++) {
-             for(i=1; i<=nlstate;i++){
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-               kk1=0.;
+        else fprintf(ficgp," %%*lf (%%*lf)");
-                 for(j=1; j<=nlstate;j++){
+      }
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-                 }
+    }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+   }
-             }
+   /*2 eme*/
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+   for (k1=1; k1<= m ; k1 ++) {
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+     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);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+     for (i=1; i<= nlstate+1 ; i ++) {
-       }
+       k=2*i;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   /******/
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         else fprintf(ficgp," %%*lf (%%*lf)");
-         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 (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-           nhstepm = nhstepm/hstepm;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           oldm=oldms;savm=savms;
+         else fprintf(ficgp," %%*lf (%%*lf)");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       }
-           for (h=0; h<=nhstepm; h++){
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       for (j=1; j<= nlstate+1 ; j ++) {
-             }
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-             for(j=1; j<=nlstate+ndeath;j++) {
+         else fprintf(ficgp," %%*lf (%%*lf)");
-               kk1=0.;kk2=0;
+       }
-               for(i=1; i<=nlstate;i++) {
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-               }
+     }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   }
-             }
-           }
+   /*3eme*/
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+   for (k1=1; k1<= m ; k1 ++) {
-       }
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-    }
+       /*       k=2+nlstate*(2*cpt-2); */
-   }
+       k=2+(nlstate+1)*(cpt-1);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-   if (popforecast==1) {
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     free_ivector(popage,0,AGESUP);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-     free_vector(popeffectif,0,AGESUP);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     free_vector(popcount,0,AGESUP);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-   }
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficrespop);
+       */
- } /* End of popforecast */
+       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);
- int fileappend(FILE *fichier, char *optionfich)
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
- {
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+       }
-     printf("Problem with file: %s\n", optionfich);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     }
-     return (0);
+   }
-   }
-   fflush(fichier);
+   /* CV preval stable (period) */
-   return (1);
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
- }
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       k=3;
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
- /**************** function prwizard **********************/
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- {
+ set ter png small size 320, 240\n\
+ unset log y\n\
-   /* Wizard to print covariance matrix template */
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       for (i=1; i<= nlstate ; i ++){
-   char ca[32], cb[32], cc[32];
+         if(i==1)
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-   int numlinepar;
+         else
+           fprintf(ficgp,", '' ");
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         l=(nlstate+ndeath)*(i-1)+1;
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   for(i=1; i <=nlstate; i++){
+         for (j=1; j<= (nlstate-1) ; j ++)
-     jj=0;
+           fprintf(ficgp,"+$%d",k+l+j);
-     for(j=1; j <=nlstate+ndeath; j++){
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-       if(j==i) continue;
+       } /* nlstate */
-       jj++;
+       fprintf(ficgp,"\n");
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+     } /* end cpt state*/
-       printf("%1d%1d",i,j);
+   } /* end covariate */
-       fprintf(ficparo,"%1d%1d",i,j);
-       for(k=1; k<=ncovmodel;k++){
+   /* proba elementaires */
-         /*        printf(" %lf",param[i][j][k]); */
+   for(i=1,jk=1; i <=nlstate; i++){
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+     for(k=1; k <=(nlstate+ndeath); k++){
-         printf(" 0.");
+       if (k != i) {
-         fprintf(ficparo," 0.");
+         for(j=1; j <=ncovmodel; j++){
-       }
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-       printf("\n");
+           jk++;
-       fprintf(ficparo,"\n");
+           fprintf(ficgp,"\n");
-     }
+         }
-   }
+       }
-   printf("# Scales (for hessian or gradient estimation)\n");
+     }
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+    }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   /*goto avoid;*/
-   for(i=1; i <=nlstate; i++){
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-     jj=0;
+      for(jk=1; jk <=m; jk++) {
-     for(j=1; j <=nlstate+ndeath; j++){
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-       if(j==i) continue;
+        if (ng==2)
-       jj++;
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-       fprintf(ficparo,"%1d%1d",i,j);
+        else
-       printf("%1d%1d",i,j);
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-       fflush(stdout);
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-       for(k=1; k<=ncovmodel;k++){
+        i=1;
-         /*      printf(" %le",delti3[i][j][k]); */
+        for(k2=1; k2<=nlstate; k2++) {
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+          k3=i;
-         printf(" 0.");
+          for(k=1; k<=(nlstate+ndeath); k++) {
-         fprintf(ficparo," 0.");
+            if (k != k2){
-       }
+              if(ng==2)
-       numlinepar++;
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-       printf("\n");
+              else
-       fprintf(ficparo,"\n");
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-     }
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-   }
+              for(j=3; j <=ncovmodel; j++) {
-   printf("# Covariance matrix\n");
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
- /* # 121 Var(a12)\n\ */
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                /*        ij++; */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                /* } */
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+                /* else */
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+              }
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+              fprintf(ficgp,")/(1");
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-   fflush(stdout);
+              for(k1=1; k1 <=nlstate; k1++){
-   fprintf(ficparo,"# Covariance matrix\n");
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-   /* # 121 Var(a12)\n\ */
+                ij=1;
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                for(j=3; j <=ncovmodel; j++){
-   /* #   ...\n\ */
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
+                  /*   ij++; */
-   for(itimes=1;itimes<=2;itimes++){
+                  /* } */
-     jj=0;
+                  /* else */
-     for(i=1; i <=nlstate; i++){
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       for(j=1; j <=nlstate+ndeath; j++){
+                }
-         if(j==i) continue;
+                fprintf(ficgp,")");
-         for(k=1; k<=ncovmodel;k++){
+              }
-           jj++;
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-           ca[0]= k+'a'-1;ca[1]='\0';
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-           if(itimes==1){
+              i=i+ncovmodel;
-             printf("#%1d%1d%d",i,j,k);
+            }
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+          } /* end k */
-           }else{
+        } /* end k2 */
-             printf("%1d%1d%d",i,j,k);
+      } /* end jk */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+    } /* end ng */
-             /*  printf(" %.5le",matcov[i][j]); */
+  /* avoid: */
-           }
+    fflush(ficgp);
-           ll=0;
+ }  /* end gnuplot */
-           for(li=1;li <=nlstate; li++){
-             for(lj=1;lj <=nlstate+ndeath; lj++){
-               if(lj==li) continue;
+ /*************** Moving average **************/
-               for(lk=1;lk<=ncovmodel;lk++){
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-                 ll++;
-                 if(ll<=jj){
+   int i, cpt, cptcod;
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+   int modcovmax =1;
-                   if(ll<jj){
+   int mobilavrange, mob;
-                     if(itimes==1){
+   double age;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-                     }else{
+                            a covariate has 2 modalities */
-                       printf(" 0.");
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-                       fprintf(ficparo," 0.");
-                     }
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-                   }else{
+     if(mobilav==1) mobilavrange=5; /* default */
-                     if(itimes==1){
+     else mobilavrange=mobilav;
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+     for (age=bage; age<=fage; age++)
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+       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.");
+     /* We keep the original values on the extreme ages bage, fage and for
-                     }
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-                   }
+        we use a 5 terms etc. until the borders are no more concerned.
-                 }
+     */
-               } /* end lk */
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-             } /* end lj */
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-           } /* end li */
+         for (i=1; i<=nlstate;i++){
-           printf("\n");
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-           fprintf(ficparo,"\n");
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-           numlinepar++;
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-         } /* end k*/
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-       } /*end j */
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-     } /* end i */
+               }
-   } /* end itimes */
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+           }
- } /* end of prwizard */
+         }
- /******************* Gompertz Likelihood ******************************/
+       }/* end age */
- double gompertz(double x[])
+     }/* end mob */
- {
+   }else return -1;
-   double A,B,L=0.0,sump=0.,num=0.;
+   return 0;
-   int i,n=0; /* n is the size of the sample */
+ }/* End movingaverage */
-   for (i=0;i<=imx-1 ; i++) {
-     sump=sump+weight[i];
+ /************** Forecasting ******************/
-     /*    sump=sump+1;*/
+ 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){
-     num=num+1;
+   /* proj1, year, month, day of starting projection
-   }
+      agemin, agemax range of age
+      dateprev1 dateprev2 range of dates during which prevalence is computed
+      anproj2 year of en of projection (same day and month as proj1).
-   /* for (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]);*/
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+   double agec; /* generic age */
-   for (i=1;i<=imx ; i++)
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-     {
+   double *popeffectif,*popcount;
-       if (cens[i] == 1 && wav[i]>1)
+   double ***p3mat;
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   double ***mobaverage;
+   char fileresf[FILENAMELENGTH];
-       if (cens[i] == 0 && wav[i]>1)
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   agelim=AGESUP;
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   strcpy(fileresf,"f");
-       if (wav[i] > 1 ) { /* ??? */
+   strcat(fileresf,fileres);
-         L=L+A*weight[i];
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-       }
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-     }
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   return -2*L*num/sump;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
- }
+   if (mobilav!=0) {
- /******************* Printing html file ***********/
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-                   int lastpass, int stepm, int weightopt, char model[],\
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-                   int imx,  double p[],double **matcov,double agemortsup){
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   int i,k;
+     }
+   }
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   for (i=1;i<=2;i++)
+   if (stepm<=12) stepsize=1;
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   if(estepm < stepm){
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   fprintf(fichtm,"</ul>");
+   }
+   else  hstepm=estepm;
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   hstepm=hstepm/stepm;
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
-  for (k=agegomp;k<(agemortsup-2);k++)
+   anprojmean=yp;
-    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]);
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-   fflush(fichtm);
+   jprojmean=yp;
- }
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
- /******************* Gnuplot file **************/
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   int ng;
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-   /*#ifdef windows */
+ /*            if (h==(int)(YEARM*yearp)){ */
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-     /*#endif */
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficresf,"\n#******");
-   strcpy(dirfileres,optionfilefiname);
+       for(j=1;j<=cptcoveff;j++) {
-   strcpy(optfileres,"vpl");
+         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(ficgp,"set out \"graphmort.png\"\n ");
+       }
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+       fprintf(ficresf,"******\n");
-   fprintf(ficgp, "set ter png small\n set log y\n");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   fprintf(ficgp, "set size 0.65,0.65\n");
+       for(j=1; j<=nlstate+ndeath;j++){
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresf," p%d%d",i,j);
- }
+         fprintf(ficresf," p.%d",j);
+       }
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
- /***********************************************/
+         for (agec=fage; agec>=(ageminpar-1); agec--){
- /**************** Main Program *****************/
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
- /***********************************************/
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- int main(int argc, char *argv[])
+           oldm=oldms;savm=savms;
- {
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+           for (h=0; h<=nhstepm; h++){
-   int linei, month, year,iout;
+             if (h*hstepm/YEARM*stepm ==yearp) {
-   int jj, ll, li, lj, lk, imk;
+               fprintf(ficresf,"\n");
-   int numlinepar=0; /* Current linenumber of parameter file */
+               for(j=1;j<=cptcoveff;j++)
-   int itimes;
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   int NDIM=2;
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+             }
-   char ca[32], cb[32], cc[32];
+             for(j=1; j<=nlstate+ndeath;j++) {
-   char dummy[]="                         ";
+               ppij=0.;
-   /*  FILE *fichtm; *//* Html File */
+               for(i=1; i<=nlstate;i++) {
-   /* FILE *ficgp;*/ /*Gnuplot File */
+                 if (mobilav==1)
-   struct stat info;
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-   double agedeb, agefin,hf;
+                 else {
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 }
-   double fret;
+                 if (h*hstepm/YEARM*stepm== yearp) {
-   double **xi,tmp,delta;
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                 }
-   double dum; /* Dummy variable */
+               } /* end i */
-   double ***p3mat;
+               if (h*hstepm/YEARM*stepm==yearp) {
-   double ***mobaverage;
+                 fprintf(ficresf," %.3f", ppij);
-   int *indx;
+               }
-   char line[MAXLINE], linepar[MAXLINE];
+             }/* end j */
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+           } /* end h */
-   char pathr[MAXLINE], pathimach[MAXLINE];
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   char **bp, *tok, *val; /* pathtot */
+         } /* end agec */
-   int firstobs=1, lastobs=10;
+       } /* end yearp */
-   int sdeb, sfin; /* Status at beginning and end */
+     } /* end cptcod */
-   int c,  h , cpt,l;
+   } /* end  cptcov */
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   fclose(ficresf);
-   int mobilav=0,popforecast=0;
+ }
-   int hstepm, nhstepm;
-   int agemortsup;
+ /************** Forecasting *****not tested NB*************/
-   float  sumlpop=0.;
+ void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
-   double bage, fage, age, agelim, agebase;
+   double calagedatem, agelim, kk1, kk2;
-   double ftolpl=FTOL;
+   double *popeffectif,*popcount;
-   double **prlim;
+   double ***p3mat,***tabpop,***tabpopprev;
-   double *severity;
+   double ***mobaverage;
-   double ***param; /* Matrix of parameters */
+   char filerespop[FILENAMELENGTH];
-   double  *p;
-   double **matcov; /* Matrix of covariance */
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double ***delti3; /* Scale */
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double *delti; /* Scale */
+   agelim=AGESUP;
-   double ***eij, ***vareij;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   double **varpl; /* Variances of prevalence limits by age */
-   double *epj, vepp;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   double **ximort;
+   strcpy(filerespop,"pop");
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   strcat(filerespop,fileres);
-   int *dcwave;
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   char z[1]="c", occ;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   char  *strt, strtend[80];
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   char *stratrunc;
-   int lstra;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   long total_usecs;
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /*   setlocale (LC_ALL, ""); */
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- /*   textdomain (PACKAGE); */
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
- /*   setlocale (LC_CTYPE, ""); */
+     }
- /*   setlocale (LC_MESSAGES, ""); */
+   }
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   (void) gettimeofday(&start_time,&tzp);
+   if (stepm<=12) stepsize=1;
-   curr_time=start_time;
-   tm = *localtime(&start_time.tv_sec);
+   agelim=AGESUP;
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+   hstepm=1;
+   hstepm=hstepm/stepm;
- /*  printf("Localtime (at start)=%s",strstart); */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+   if (popforecast==1) {
- /*  tm = *localtime(&start_time.tv_sec); */
+     if((ficpop=fopen(popfile,"r"))==NULL) {
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       printf("Problem with population file : %s\n",popfile);exit(0);
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+     }
- /*   tp.tv_sec = mktime(&tmg); */
+     popage=ivector(0,AGESUP);
- /*   strt=asctime(&tmg); */
+     popeffectif=vector(0,AGESUP);
- /*   printf("Time(after) =%s",strstart);  */
+     popcount=vector(0,AGESUP);
- /*  (void) time (&time_value);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+     i=1;
- *  tm = *localtime(&time_value);
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
- *  strstart=asctime(&tm);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+     imx=i;
- */
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
-   nberr=0; /* Number of errors and warnings */
-   nbwarn=0;
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-   getcwd(pathcd, size);
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
-   printf("\n%s\n%s",version,fullversion);
+       fprintf(ficrespop,"\n#******");
-   if(argc <=1){
+       for(j=1;j<=cptcoveff;j++) {
-     printf("\nEnter the parameter file name: ");
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     fgets(pathr,FILENAMELENGTH,stdin);
+       }
-     i=strlen(pathr);
+       fprintf(ficrespop,"******\n");
-     if(pathr[i-1]=='\n')
+       fprintf(ficrespop,"# Age");
-       pathr[i-1]='\0';
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-    for (tok = pathr; tok != NULL; ){
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-       printf("Pathr |%s|\n",pathr);
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       for (cpt=0; cpt<=0;cpt++) {
-       printf("val= |%s| pathr=%s\n",val,pathr);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-       strcpy (pathtot, val);
-       if(pathr[0] == '\0') break; /* Dirty */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-     }
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   }
+           nhstepm = nhstepm/hstepm;
-   else{
-     strcpy(pathtot,argv[1]);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
+           oldm=oldms;savm=savms;
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   /*cygwin_split_path(pathtot,path,optionfile);
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+           for (h=0; h<=nhstepm; h++){
-   /* cutv(path,optionfile,pathtot,'\\');*/
+             if (h==(int) (calagedatem+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   /* Split argv[0], imach program to get pathimach */
+             }
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+             for(j=1; j<=nlstate+ndeath;j++) {
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+               kk1=0.;kk2=0;
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+               for(i=1; i<=nlstate;i++) {
-  /*   strcpy(pathimach,argv[0]); */
+                 if (mobilav==1)
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+                 else {
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-   chdir(path); /* Can be a relative path */
+                 }
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+               }
-     printf("Current directory %s!\n",pathcd);
+               if (h==(int)(calagedatem+12*cpt)){
-   strcpy(command,"mkdir ");
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   strcat(command,optionfilefiname);
+                   /*fprintf(ficrespop," %.3f", kk1);
-   if((outcmd=system(command)) != 0){
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-     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(i=1; i<=nlstate;i++){
- /*     exit(1); */
+               kk1=0.;
-   }
+                 for(j=1; j<=nlstate;j++){
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
- /*     perror("mkdir"); */
+                 }
- /*   } */
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
-   /*-------- arguments in the command line --------*/
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   /* Log file */
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   strcat(filelog, optionfilefiname);
+           }
-   strcat(filelog,".log");    /* */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+         }
-     printf("Problem with logfile %s\n",filelog);
+       }
-     goto end;
-   }
+   /******/
-   fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-  path=%s \n\
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-  optionfile=%s\n\
+           nhstepm = nhstepm/hstepm;
-  optionfilext=%s\n\
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
-   printf("Local time (at start):%s",strstart);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+           for (h=0; h<=nhstepm; h++){
-   fflush(ficlog);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
- /*   (void) gettimeofday(&curr_time,&tzp); */
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
-   /* */
+               kk1=0.;kk2=0;
-   strcpy(fileres,"r");
+               for(i=1; i<=nlstate;i++) {
-   strcat(fileres, optionfilefiname);
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   strcat(fileres,".txt");    /* Other files have txt extension */
+               }
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   /*---------arguments file --------*/
+             }
+           }
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("Problem with optionfile %s\n",optionfile);
+         }
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+       }
-     fflush(ficlog);
+    }
-     goto end;
+   }
-   }
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (popforecast==1) {
-   strcpy(filereso,"o");
+     free_ivector(popage,0,AGESUP);
-   strcat(filereso,fileres);
+     free_vector(popeffectif,0,AGESUP);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+     free_vector(popcount,0,AGESUP);
-     printf("Problem with Output resultfile: %s\n", filereso);
+   }
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     fflush(ficlog);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     goto end;
+   fclose(ficrespop);
-   }
+ } /* End of popforecast */
-   /* Reads comments: lines beginning with '#' */
+ int fileappend(FILE *fichier, char *optionfich)
-   numlinepar=0;
+ {
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-     ungetc(c,ficpar);
+     printf("Problem with file: %s\n", optionfich);
-     fgets(line, MAXLINE, ficpar);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-     numlinepar++;
+     return (0);
-     puts(line);
+   }
-     fputs(line,ficparo);
+   fflush(fichier);
-     fputs(line,ficlog);
+   return (1);
-   }
+ }
-   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);
+ /**************** function prwizard **********************/
-   numlinepar++;
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+ {
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-   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);
+   /* Wizard to print covariance matrix template */
-   fflush(ficlog);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   char ca[32], cb[32];
-     ungetc(c,ficpar);
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-     fgets(line, MAXLINE, ficpar);
+   int numlinepar;
-     numlinepar++;
-     puts(line);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fputs(line,ficparo);
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fputs(line,ficlog);
+   for(i=1; i <=nlstate; i++){
-   }
+     jj=0;
-   ungetc(c,ficpar);
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
-   covar=matrix(0,NCOVMAX,1,n);
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       printf("%1d%1d",i,j);
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       fprintf(ficparo,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+         /*        printf(" %lf",param[i][j][k]); */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         printf(" 0.");
+         fprintf(ficparo," 0.");
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       }
-   delti=delti3[1][1];
+       printf("\n");
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+       fprintf(ficparo,"\n");
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+     }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+   }
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   printf("# Scales (for hessian or gradient estimation)\n");
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     fclose (ficparo);
+   for(i=1; i <=nlstate; i++){
-     fclose (ficlog);
+     jj=0;
-     goto end;
+     for(j=1; j <=nlstate+ndeath; j++){
-     exit(0);
+       if(j==i) continue;
-   }
+       jj++;
-   else if(mle==-3) {
+       fprintf(ficparo,"%1d%1d",i,j);
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+       printf("%1d%1d",i,j);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       fflush(stdout);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       for(k=1; k<=ncovmodel;k++){
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         /*      printf(" %le",delti3[i][j][k]); */
-     matcov=matrix(1,npar,1,npar);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   }
+         printf(" 0.");
-   else{
+         fprintf(ficparo," 0.");
-     /* Read guess parameters */
+       }
-     /* Reads comments: lines beginning with '#' */
+       numlinepar++;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       printf("\n");
-       ungetc(c,ficpar);
+       fprintf(ficparo,"\n");
-       fgets(line, MAXLINE, ficpar);
+     }
-       numlinepar++;
+   }
-       puts(line);
+   printf("# Covariance matrix\n");
-       fputs(line,ficparo);
+ /* # 121 Var(a12)\n\ */
-       fputs(line,ficlog);
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     }
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     ungetc(c,ficpar);
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     for(i=1; i <=nlstate; i++){
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-       j=0;
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+   fflush(stdout);
-         if(jj==i) continue;
+   fprintf(ficparo,"# Covariance matrix\n");
-         j++;
+   /* # 121 Var(a12)\n\ */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-         if ((i1 != i) && (j1 != j)){
+   /* #   ...\n\ */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
- It might be a problem of design; if ncovcol and the model are correct\n \
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+   for(itimes=1;itimes<=2;itimes++){
-           exit(1);
+     jj=0;
-         }
+     for(i=1; i <=nlstate; i++){
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       for(j=1; j <=nlstate+ndeath; j++){
-         if(mle==1)
+         if(j==i) continue;
-           printf("%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
-         fprintf(ficlog,"%1d%1d",i,j);
+           jj++;
-         for(k=1; k<=ncovmodel;k++){
+           ca[0]= k+'a'-1;ca[1]='\0';
-           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(itimes==1){
-           if(mle==1){
+             printf("#%1d%1d%d",i,j,k);
-             printf(" %lf",param[i][j][k]);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-             fprintf(ficlog," %lf",param[i][j][k]);
+           }else{
-           }
+             printf("%1d%1d%d",i,j,k);
-           else
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-             fprintf(ficlog," %lf",param[i][j][k]);
+             /*  printf(" %.5le",matcov[i][j]); */
-           fprintf(ficparo," %lf",param[i][j][k]);
+           }
-         }
+           ll=0;
-         fscanf(ficpar,"\n");
+           for(li=1;li <=nlstate; li++){
-         numlinepar++;
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-         if(mle==1)
+               if(lj==li) continue;
-           printf("\n");
+               for(lk=1;lk<=ncovmodel;lk++){
-         fprintf(ficlog,"\n");
+                 ll++;
-         fprintf(ficparo,"\n");
+                 if(ll<=jj){
-       }
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-     }
+                   if(ll<jj){
-     fflush(ficlog);
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     p=param[1][1];
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
-     /* Reads comments: lines beginning with '#' */
+                       printf(" 0.");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+                       fprintf(ficparo," 0.");
-       ungetc(c,ficpar);
+                     }
-       fgets(line, MAXLINE, ficpar);
+                   }else{
-       numlinepar++;
+                     if(itimes==1){
-       puts(line);
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-       fputs(line,ficparo);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-       fputs(line,ficlog);
+                     }else{
-     }
+                       printf(" 0.");
-     ungetc(c,ficpar);
+                       fprintf(ficparo," 0.");
+                     }
-     for(i=1; i <=nlstate; i++){
+                   }
-       for(j=1; j <=nlstate+ndeath-1; j++){
+                 }
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+               } /* end lk */
-         if ((i1-i)*(j1-j)!=0){
+             } /* end lj */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           } /* end li */
-           exit(1);
+           printf("\n");
-         }
+           fprintf(ficparo,"\n");
-         printf("%1d%1d",i,j);
+           numlinepar++;
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         } /* end k*/
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       } /*end j */
-         for(k=1; k<=ncovmodel;k++){
+     } /* end i */
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+   } /* end itimes */
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+ } /* end of prwizard */
-           fprintf(ficlog," %le",delti3[i][j][k]);
+ /******************* Gompertz Likelihood ******************************/
-         }
+ double gompertz(double x[])
-         fscanf(ficpar,"\n");
+ {
-         numlinepar++;
+   double A,B,L=0.0,sump=0.,num=0.;
-         printf("\n");
+   int i,n=0; /* n is the size of the sample */
-         fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+   for (i=0;i<=imx-1 ; i++) {
-       }
+     sump=sump+weight[i];
-     }
+     /*    sump=sump+1;*/
-     fflush(ficlog);
+     num=num+1;
+   }
-     delti=delti3[1][1];
+   /* for (i=0; i<=imx; i++)
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+      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]);*/
-     /* Reads comments: lines beginning with '#' */
+   for (i=1;i<=imx ; i++)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     {
-       ungetc(c,ficpar);
+       if (cens[i] == 1 && wav[i]>1)
-       fgets(line, MAXLINE, ficpar);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-       numlinepar++;
-       puts(line);
+       if (cens[i] == 0 && wav[i]>1)
-       fputs(line,ficparo);
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-       fputs(line,ficlog);
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-     }
-     ungetc(c,ficpar);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
-     matcov=matrix(1,npar,1,npar);
+         L=L+A*weight[i];
-     for(i=1; i <=npar; i++){
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-       fscanf(ficpar,"%s",&str);
+       }
-       if(mle==1)
+     }
-         printf("%s",str);
-       fprintf(ficlog,"%s",str);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       fprintf(ficparo,"%s",str);
-       for(j=1; j <=i; j++){
+   return -2*L*num/sump;
-         fscanf(ficpar," %le",&matcov[i][j]);
+ }
-         if(mle==1){
-           printf(" %.5le",matcov[i][j]);
+ #ifdef GSL
-         }
+ /******************* Gompertz_f Likelihood ******************************/
-         fprintf(ficlog," %.5le",matcov[i][j]);
+ double gompertz_f(const gsl_vector *v, void *params)
-         fprintf(ficparo," %.5le",matcov[i][j]);
+ {
-       }
+   double A,B,LL=0.0,sump=0.,num=0.;
-       fscanf(ficpar,"\n");
+   double *x= (double *) v->data;
-       numlinepar++;
+   int i,n=0; /* n is the size of the sample */
-       if(mle==1)
-         printf("\n");
+   for (i=0;i<=imx-1 ; i++) {
-       fprintf(ficlog,"\n");
+     sump=sump+weight[i];
-       fprintf(ficparo,"\n");
+     /*    sump=sump+1;*/
-     }
+     num=num+1;
-     for(i=1; i <=npar; i++)
+   }
-       for(j=i+1;j<=npar;j++)
-         matcov[i][j]=matcov[j][i];
+   /* 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("\n");
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     fprintf(ficlog,"\n");
+   for (i=1;i<=imx ; i++)
+     {
-     fflush(ficlog);
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+       if (cens[i] == 0 && wav[i]>1)
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-     strcat(rfileres,".");    /* */
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       if (wav[i] > 1 ) { /* ??? */
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+         LL=LL+A*weight[i];
-     }
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-     fprintf(ficres,"#%s\n",version);
+       }
-   }    /* End of mle != -3 */
+     }
-   /*-------- data file ----------*/
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   return -2*LL*num/sump;
-   }
+ }
+ #endif
-   n= lastobs;
-   severity = vector(1,maxwav);
+ /******************* Printing html file ***********/
-   outcome=imatrix(1,maxwav+1,1,n);
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   num=lvector(1,n);
+                   int lastpass, int stepm, int weightopt, char model[],\
-   moisnais=vector(1,n);
+                   int imx,  double p[],double **matcov,double agemortsup){
-   annais=vector(1,n);
+   int i,k;
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-   agedc=vector(1,n);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   cod=ivector(1,n);
+   for (i=1;i<=2;i++)
-   weight=vector(1,n);
+     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]));
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   mint=matrix(1,maxwav,1,n);
+   fprintf(fichtm,"</ul>");
-   anint=matrix(1,maxwav,1,n);
-   s=imatrix(1,maxwav+1,1,n);
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+  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>");
-   i=1;
+  for (k=agegomp;k<(agemortsup-2);k++)
-   linei=0;
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     linei=linei+1;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+   fflush(fichtm);
-       if(line[j] == '\t')
+ }
-         line[j] = ' ';
-     }
+ /******************* Gnuplot file **************/
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       ;
-     };
+   char dirfileres[132],optfileres[132];
-     line[j+1]=0;  /* Trims blanks at end of line */
-     if(line[0]=='#'){
+   int ng;
-       fprintf(ficlog,"Comment line\n%s\n",line);
-       printf("Comment line\n%s\n",line);
-       continue;
+   /*#ifdef windows */
-     }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
-     for (j=maxwav;j>=1;j--){
-       cutv(stra, strb,line,' ');
-       errno=0;
+   strcpy(dirfileres,optionfilefiname);
-       lval=strtol(strb,&endptr,10);
+   strcpy(optfileres,"vpl");
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-         exit(1);
+   /* 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);
-       s[j][i]=lval;
+ }
-       strcpy(line,stra);
-       cutv(stra, strb,line,' ');
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ {
-       }
-       else  if(iout=sscanf(strb,"%s.") != 0){
+   /*-------- data file ----------*/
-         month=99;
+   FILE *fic;
-         year=9999;
+   char dummy[]="                         ";
-       }else{
+   int i=0, j=0, n=0;
-         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);
+   int linei, month, year,iout;
-         exit(1);
+   char line[MAXLINE], linetmp[MAXLINE];
-       }
+   char stra[MAXLINE], strb[MAXLINE];
-       anint[j][i]= (double) year;
+   char *stratrunc;
-       mint[j][i]= (double)month;
+   int lstra;
-       strcpy(line,stra);
-     } /* ENd Waves */
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     cutv(stra, strb,line,' ');
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-     }
+   }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-       month=99;
+   i=1;
-       year=9999;
+   linei=0;
-     }else{
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+     linei=linei+1;
-       exit(1);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     }
+       if(line[j] == '\t')
-     andc[i]=(double) year;
+         line[j] = ' ';
-     moisdc[i]=(double) month;
+     }
-     strcpy(line,stra);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
-     cutv(stra, strb,line,' ');
+     };
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     line[j+1]=0;  /* Trims blanks at end of line */
-     }
+     if(line[0]=='#'){
-     else  if(iout=sscanf(strb,"%s.") != 0){
+       fprintf(ficlog,"Comment line\n%s\n",line);
-       month=99;
+       printf("Comment line\n%s\n",line);
-       year=9999;
+       continue;
-     }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);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       exit(1);
+     strcpy(line, linetmp);
-     }
-     annais[i]=(double)(year);
-     moisnais[i]=(double)(month);
+     for (j=maxwav;j>=1;j--){
-     strcpy(line,stra);
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
-     cutv(stra, strb,line,' ');
+         lval=-1;
-     errno=0;
+       }else{
-     dval=strtod(strb,&endptr);
+         errno=0;
-     if( strb[0]=='\0' || (*endptr != '\0')){
+         lval=strtol(strb,&endptr,10);
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       exit(1);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     }
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-     weight[i]=dval;
+           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);
-     strcpy(line,stra);
+           return 1;
+         }
-     for (j=ncovcol;j>=1;j--){
+       }
-       cutv(stra, strb,line,' ');
+       s[j][i]=lval;
-       errno=0;
-       lval=strtol(strb,&endptr,10);
+       strcpy(line,stra);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       cutv(stra, strb,line,' ');
-         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);
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-         exit(1);
+       }
-       }
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-       if(lval <-1 || lval >1){
+         month=99;
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+         year=9999;
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+       }else{
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+         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);
-  For example, for multinomial values like 1, 2 and 3,\n \
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
-  build V1=0 V2=0 for the reference value (1),\n \
+         return 1;
-         V1=1 V2=0 for (2) \n \
+       }
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+       anint[j][i]= (double) year;
-  output of IMaCh is often meaningless.\n \
+       mint[j][i]= (double)month;
-  Exiting.\n",lval,linei, i,line,j);
+       strcpy(line,stra);
-         exit(1);
+     } /* ENd Waves */
-       }
-       covar[j][i]=(double)(lval);
+     cutv(stra, strb,line,' ');
-       strcpy(line,stra);
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     lstra=strlen(stra);
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
+       month=99;
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       year=9999;
-       stratrunc = &(stra[lstra-9]);
+     }else{
-       num[i]=atol(stratrunc);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-     }
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     else
+         return 1;
-       num[i]=atol(stra);
+     }
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+     andc[i]=(double) year;
-       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;}*/
+     moisdc[i]=(double) month;
+     strcpy(line,stra);
-     i=i+1;
-   } /* End loop reading  data */
+     cutv(stra, strb,line,' ');
-   fclose(fic);
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
-   /* printf("ii=%d", ij);
+     }
-      scanf("%d",i);*/
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
-   imx=i-1; /* Number of individuals */
+       month=99;
+       year=9999;
-   /* for (i=1; i<=imx; i++){
+     }else{
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+       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);
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+       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);
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+         return 1;
-     }*/
+     }
-    /*  for (i=1; i<=imx; i++){
+     if (year==9999) {
-      if (s[4][i]==9)  s[4][i]=-1;
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-      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]));}*/
+       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);
+         return 1;
-   /* for (i=1; i<=imx; i++) */
+     }
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+     annais[i]=(double)(year);
-      else weight[i]=1;*/
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
-   /* Calculation of the number of parameters from char model */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+     cutv(stra, strb,line,' ');
-   Tprod=ivector(1,15);
+     errno=0;
-   Tvaraff=ivector(1,15);
+     dval=strtod(strb,&endptr);
-   Tvard=imatrix(1,15,1,2);
+     if( strb[0]=='\0' || (*endptr != '\0')){
-   Tage=ivector(1,15);
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+       fflush(ficlog);
-     j=0, j1=0, k1=1, k2=1;
+       return 1;
-     j=nbocc(model,'+'); /* j=Number of '+' */
+     }
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     weight[i]=dval;
-     cptcovn=j+1;
+     strcpy(line,stra);
-     cptcovprod=j1; /*Number of products */
+     for (j=ncovcol;j>=1;j--){
-     strcpy(modelsav,model);
+       cutv(stra, strb,line,' ');
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+       if(strb[0]=='.') { /* Missing status */
-       printf("Error. Non available option model=%s ",model);
+         lval=-1;
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       }else{
-       goto end;
+         errno=0;
-     }
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     /* This loop fills the array Tvar from the string 'model'.*/
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(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);
-     for(i=(j+1); i>=1;i--){
+           return 1;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+         }
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       }
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       if(lval <-1 || lval >1){
-       /*scanf("%d",i);*/
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-       if (strchr(strb,'*')) {  /* Model includes a product */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+  For example, for multinomial values like 1, 2 and 3,\n \
-           cptcovprod--;
+  build V1=0 V2=0 for the reference value (1),\n \
-           cutv(strb,stre,strd,'V');
+         V1=1 V2=0 for (2) \n \
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-           cptcovage++;
+  output of IMaCh is often meaningless.\n \
-             Tage[cptcovage]=i;
+  Exiting.\n",lval,linei, i,line,j);
-             /*printf("stre=%s ", stre);*/
+         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 \
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-           cptcovprod--;
+  For example, for multinomial values like 1, 2 and 3,\n \
-           cutv(strb,stre,strc,'V');
+  build V1=0 V2=0 for the reference value (1),\n \
-           Tvar[i]=atoi(stre);
+         V1=1 V2=0 for (2) \n \
-           cptcovage++;
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-           Tage[cptcovage]=i;
+  output of IMaCh is often meaningless.\n \
-         }
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-         else {  /* Age is not in the model */
+         return 1;
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+       }
-           Tvar[i]=ncovcol+k1;
+       covar[j][i]=(double)(lval);
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+       strcpy(line,stra);
-           Tprod[k1]=i;
+     }
-           Tvard[k1][1]=atoi(strc); /* m*/
+     lstra=strlen(stra);
-           Tvard[k1][2]=atoi(stre); /* n */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+       stratrunc = &(stra[lstra-9]);
-           for (k=1; k<=lastobs;k++)
+       num[i]=atol(stratrunc);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+     }
-           k1++;
+     else
-           k2=k2+2;
+       num[i]=atol(stra);
-         }
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       }
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-       else { /* no more sum */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+     i=i+1;
-        /*  scanf("%d",i);*/
+   } /* End loop reading  data */
-       cutv(strd,strc,strb,'V');
-       Tvar[i]=atoi(strc);
+   *imax=i-1; /* Number of individuals */
-       }
+   fclose(fic);
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+   return (0);
-         scanf("%d",i);*/
+   /* endread: */
-     } /* end of loop + */
+     printf("Exiting readdata: ");
-   } /* end model */
+     fclose(fic);
+     return (1);
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ }
-   printf("cptcovprod=%d ", cptcovprod);
+ void removespace(char *str) {
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   char *p1 = str, *p2 = str;
+   do
-   scanf("%d ",i);*/
+     while (*p2 == ' ')
+       p2++;
-     /*  if(mle==1){*/
+   while (*p1++ == *p2++);
-   if (weightopt != 1) { /* Maximisation without weights*/
+ }
-     for(i=1;i<=n;i++) weight[i]=1.0;
-   }
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-     /*-calculation of age at interview from date of interview and age at death -*/
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-   agev=matrix(1,maxwav,1,imx);
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-   for (i=1; i<=imx; i++) {
+    * - cptcovage number of covariates with age*products =2
-     for(m=2; (m<= maxwav); m++) {
+    * - cptcovs number of simple covariates
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+    * - 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
-         anint[m][i]=9999;
+    *     which is a new column after the 9 (ncovcol) variables.
-         s[m][i]=-1;
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-       }
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-         nberr++;
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+  */
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+ {
-         s[m][i]=-1;
+   int i, j, k, ks;
-       }
+   int  j1, k1, k2;
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+   char modelsav[80];
-         nberr++;
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-         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]);
+   /*removespace(model);*/
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-       }
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     }
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-   }
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-   for (i=1; i<=imx; i++)  {
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+                   /* including age products which are counted in cptcovage.
-     for(m=firstpass; (m<= lastpass); m++){
+                   * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-         if (s[m][i] >= nlstate+1) {
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-           if(agedc[i]>0)
+     strcpy(modelsav,model);
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     if (strstr(model,"AGE") !=0){
-               agev[m][i]=agedc[i];
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-             else {
+       return 1;
-               if ((int)andc[i]!=9999){
+     }
-                 nbwarn++;
+     if (strstr(model,"v") !=0){
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-                 agev[m][i]=-1;
+       return 1;
-               }
+     }
-             }
-         }
+     /*   Design
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-                                  years but with the precision of a month */
+      *  <          ncovcol=8                >
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+      *   k=  1    2      3       4     5       6      7        8
-             agev[m][i]=1;
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-           else if(agev[m][i] <agemin){
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-             agemin=agev[m][i];
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-           }
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-           else if(agev[m][i] >agemax){
+      *  Tage[++cptcovage]=k
-             agemax=agev[m][i];
+      *       if products, new covar are created after ncovcol with k1
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-           }
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+      *  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
-           /*     agev[m][i] = age[i]+2*m;*/
+      *  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
-         else { /* =9 */
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-           agev[m][i]=1;
+      *  <          ncovcol=8                >
-           s[m][i]=-1;
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-         }
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-       }
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-       else /*= 0 Unknown */
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         agev[m][i]=1;
+      * p Tprod[1]@2={                         6, 5}
-     }
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-   }
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   for (i=1; i<=imx; i++)  {
+      *How to reorganize?
-     for(m=firstpass; (m<=lastpass); m++){
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-       if (s[m][i] > (nlstate+ndeath)) {
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         nberr++;
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-         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);
+      * Struct []
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+      */
-         goto end;
-       }
+     /* This loop fills the array Tvar from the string 'model'.*/
-     }
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-   }
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-   /*for (i=1; i<=imx; i++){
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-   for (m=firstpass; (m<lastpass); m++){
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+     /*  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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     /*
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-   agegomp=(int)agemin;
+         Tvar[k]=0;
-   free_vector(severity,1,maxwav);
+     cptcovage=0;
-   free_imatrix(outcome,1,maxwav+1,1,n);
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-   free_vector(moisnais,1,n);
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-   free_vector(annais,1,n);
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-   /* free_matrix(mint,1,maxwav,1,n);
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-      free_matrix(anint,1,maxwav,1,n);*/
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-   free_vector(moisdc,1,n);
+       /*scanf("%d",i);*/
-   free_vector(andc,1,n);
+       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 */
-   wav=ivector(1,imx);
+           /* covar is not filled and then is empty */
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+           cptcovprod--;
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-   /* Concatenates waves */
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+           /*printf("stre=%s ", stre);*/
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+           cptcovprod--;
+           cutl(stre,strb,strc,'V');
-   Tcode=ivector(1,100);
+           Tvar[k]=atoi(stre);
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+           cptcovage++;
-   ncodemax[1]=1;
+           Tage[cptcovage]=k;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+           cptcovn++;
-                                  the estimations*/
+           cptcovprodnoage++;k1++;
-   h=0;
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   m=pow(2,cptcoveff);
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+                                   because this model-covariate is a construction we invent a new column
-   for(k=1;k<=cptcoveff; k++){
+                                   ncovcol + k1
-     for(i=1; i <=(m/pow(2,k));i++){
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-       for(j=1; j <= ncodemax[k]; j++){
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-           h++;
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-         }
+           k2=k2+2;
-       }
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-     }
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-   }
+           for (i=1; i<=lastobs;i++){
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+             /* Computes the new covariate which is a product of
-      codtab[1][2]=1;codtab[2][2]=2; */
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-   /* for(i=1; i <=m ;i++){
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-      for(k=1; k <=cptcovn; k++){
+           }
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+         } /* End age is not in the model */
-      }
+       } /* End if model includes a product */
-      printf("\n");
+       else { /* no more sum */
-      }
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-      scanf("%d",i);*/
+        /*  scanf("%d",i);*/
+         cutl(strd,strc,strb,'V');
-   /*------------ gnuplot -------------*/
+         ks++; /**< Number of simple covariates */
-   strcpy(optionfilegnuplot,optionfilefiname);
+         cptcovn++;
-   if(mle==-3)
+         Tvar[k]=atoi(strd);
-     strcat(optionfilegnuplot,"-mort");
+       }
-   strcat(optionfilegnuplot,".gp");
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+         scanf("%d",i);*/
-     printf("Problem with file %s",optionfilegnuplot);
+     } /* end of loop + */
-   }
+   } /* end model */
-   else{
-     fprintf(ficgp,"\n# %s\n", version);
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-     fprintf(ficgp,"set missing 'NaNq'\n");
-   }
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   /*  fclose(ficgp);*/
+   printf("cptcovprod=%d ", cptcovprod);
-   /*--------- index.htm --------*/
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   scanf("%d ",i);*/
-   if(mle==-3)
-     strcat(optionfilehtm,"-mort");
-   strcat(optionfilehtm,".htm");
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+   /*endread:*/
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     printf("Exiting decodemodel: ");
-   }
+     return (1);
+ }
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-   strcat(optionfilehtmcov,"-cov.htm");
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+ {
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   int i, m;
-   }
-   else{
+   for (i=1; i<=imx; i++) {
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     for(m=2; (m<= maxwav); m++) {
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+         anint[m][i]=9999;
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+         s[m][i]=-1;
-   }
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+         *nberr = *nberr + 1;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
- \n\
+         s[m][i]=-1;
- <hr  size=\"2\" color=\"#EC5E5E\">\
+       }
-  <ul><li><h4>Parameter files</h4>\n\
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+         (*nberr)++;
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+         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]);
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-  - Date and time at start: %s</ul>\n",\
+       }
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+     }
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+   }
-           fileres,fileres,\
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   for (i=1; i<=imx; i++)  {
-   fflush(fichtm);
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
-   strcpy(pathr,path);
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-   strcat(pathr,optionfilefiname);
+         if (s[m][i] >= nlstate+1) {
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           if(agedc[i]>0){
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+               agev[m][i]=agedc[i];
-      and prints on file fileres'p'. */
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+             }else {
+               if ((int)andc[i]!=9999){
-   fprintf(fichtm,"\n");
+                 nbwarn++;
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+                 agev[m][i]=-1;
-           imx,agemin,agemax,jmin,jmax,jmean);
+               }
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+             }
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           } /* agedc > 0 */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         }
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+             agev[m][i]=1;
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+           else if(agev[m][i] < *agemin){
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+           }
+           else if(agev[m][i] >*agemax){
-   if (mle==-3){
+             *agemax=agev[m][i];
-     ximort=matrix(1,NDIM,1,NDIM);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-     cens=ivector(1,n);
+           }
-     ageexmed=vector(1,n);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-     agecens=vector(1,n);
+           /*     agev[m][i] = age[i]+2*m;*/
-     dcwave=ivector(1,n);
+         }
+         else { /* =9 */
-     for (i=1; i<=imx; i++){
+           agev[m][i]=1;
-       dcwave[i]=-1;
+           s[m][i]=-1;
-       for (m=firstpass; m<=lastpass; m++)
+         }
-         if (s[m][i]>nlstate) {
+       }
-           dcwave[i]=m;
+       else /*= 0 Unknown */
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+         agev[m][i]=1;
-           break;
+     }
-         }
-     }
+   }
+   for (i=1; i<=imx; i++)  {
-     for (i=1; i<=imx; i++) {
+     for(m=firstpass; (m<=lastpass); m++){
-       if (wav[i]>0){
+       if (s[m][i] > (nlstate+ndeath)) {
-         ageexmed[i]=agev[mw[1][i]][i];
+         (*nberr)++;
-         j=wav[i];
+         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[i]=1.;
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 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;
+   /*for (i=1; i<=imx; i++){
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   for (m=firstpass; (m<lastpass); m++){
-           cens[i]=0 ;
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-       }
+ }
-       else cens[i]=-1;
-     }
+ }*/
-     for (i=1;i<=NDIM;i++) {
-       for (j=1;j<=NDIM;j++)
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     }
+   return (0);
-     p[1]=0.0268; p[NDIM]=0.083;
+  /* endread:*/
-     /*printf("%lf %lf", p[1], p[2]);*/
+     printf("Exiting calandcheckages: ");
+     return (1);
+ }
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     strcpy(filerespow,"pow-mort");
+ #if defined(_MSC_VER)
-     strcat(filerespow,fileres);
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
-       printf("Problem with resultfile: %s\n", filerespow);
+ //#include "stdafx.h"
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ //#include <stdio.h>
-     }
+ //#include <tchar.h>
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ //#include <windows.h>
-     /*  for (i=1;i<=nlstate;i++)
+ //#include <iostream>
-         for(j=1;j<=nlstate+ndeath;j++)
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     */
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
-     fprintf(ficrespow,"\n");
+ BOOL IsWow64()
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ {
-     fclose(ficrespow);
+         BOOL bIsWow64 = FALSE;
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
+         //  (HANDLE, PBOOL);
-     for(i=1; i <=NDIM; i++)
-       for(j=i+1;j<=NDIM;j++)
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
-         matcov[i][j]=matcov[j][i];
+         HMODULE module = GetModuleHandle(_T("kernel32"));
-     printf("\nCovariance matrix\n ");
+         const char funcName[] = "IsWow64Process";
-     for(i=1; i <=NDIM; i++) {
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
-       for(j=1;j<=NDIM;j++){
+                 GetProcAddress(module, funcName);
-         printf("%f ",matcov[i][j]);
-       }
+         if (NULL != fnIsWow64Process)
-       printf("\n ");
+         {
-     }
+                 if (!fnIsWow64Process(GetCurrentProcess(),
+                         &bIsWow64))
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+                         //throw std::exception("Unknown error");
-     for (i=1;i<=NDIM;i++)
+                         printf("Unknown error\n");
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+         }
+         return bIsWow64 != FALSE;
-     lsurv=vector(1,AGESUP);
+ }
-     lpop=vector(1,AGESUP);
+ #endif
-     tpop=vector(1,AGESUP);
-     lsurv[agegomp]=100000;
+ void syscompilerinfo()
+  {
-     for (k=agegomp;k<=AGESUP;k++) {
+    /* #include "syscompilerinfo.h"*/
-       agemortsup=k;
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+ #if defined __INTEL_COMPILER
-     }
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
-     for (k=agegomp;k<agemortsup;k++)
+ #endif
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
-     for (k=agegomp;k<agemortsup;k++){
+ #include <gnu/libc-version.h>  /* Only on gnu */
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+ #endif
-       sumlpop=sumlpop+lpop[k];
+    struct utsname sysInfo;
-     }
+    int cross = CROSS;
+    if (cross){
-     tpop[agegomp]=sumlpop;
+            printf("Cross-");
-     for (k=agegomp;k<(agemortsup-3);k++){
+            fprintf(ficlog, "Cross-");
-       /*  tpop[k+1]=2;*/
+    }
-       tpop[k+1]=tpop[k]-lpop[k];
+ #endif
-     }
+ #include <stdint.h>
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
-     for (k=agegomp;k<(agemortsup-2);k++)
+ #if defined(__clang__)
-       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]);
+    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
-                      stepm, weightopt,\
+ #endif
-                      model,imx,p,matcov,agemortsup);
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
-     free_vector(lsurv,1,AGESUP);
+ #endif
-     free_vector(lpop,1,AGESUP);
+ #if defined(__IBMC__) || defined(__IBMCPP__)
-     free_vector(tpop,1,AGESUP);
+    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
-   } /* Endof if mle==-3 */
+ #endif
+ #if defined(_MSC_VER)
-   else{ /* For mle >=1 */
+    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ #if defined(__PGI)
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
-     for (k=1; k<=npar;k++)
+ #endif
-       printf(" %d %8.5f",k,p[k]);
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-     printf("\n");
+    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
-     globpr=1; /* to print the contributions */
+ #endif
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+    printf(" for ");fprintf(ficlog," for ");
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
-       printf(" %d %8.5f",k,p[k]);
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
-     printf("\n");
+     // Windows (x64 and x86)
-     if(mle>=1){ /* Could be 1 or 2 */
+    printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+ #elif __unix__ // all unices, not all compilers
-     }
+     // Unix
+    printf("Unix ");fprintf(ficlog,"Unix ");
-     /*--------- results files --------------*/
+ #elif __linux__
-     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);
+     // linux
+    printf("linux ");fprintf(ficlog,"linux ");
+ #elif __APPLE__
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+    printf("Mac OS ");fprintf(ficlog,"Mac OS ");
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ #endif
-     for(i=1,jk=1; i <=nlstate; i++){
-       for(k=1; k <=(nlstate+ndeath); k++){
+ /*  __MINGW32__   */
-         if (k != i) {
+ /*  __CYGWIN__   */
-           printf("%d%d ",i,k);
+ /* __MINGW64__  */
-           fprintf(ficlog,"%d%d ",i,k);
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
-           fprintf(ficres,"%1d%1d ",i,k);
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
-           for(j=1; j <=ncovmodel; j++){
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
-             printf("%lf ",p[jk]);
+ /* _WIN64  // Defined for applications for Win64. */
-             fprintf(ficlog,"%lf ",p[jk]);
+ /* _M_X64 // Defined for compilations that target x64 processors. */
-             fprintf(ficres,"%lf ",p[jk]);
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
-             jk++;
-           }
+ #if UINTPTR_MAX == 0xffffffff
-           printf("\n");
+    printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
-           fprintf(ficlog,"\n");
+ #elif UINTPTR_MAX == 0xffffffffffffffff
-           fprintf(ficres,"\n");
+    printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
-         }
+ #else
-       }
+    printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
-     }
+ #endif
-     if(mle!=0){
-       /* Computing hessian and covariance matrix */
+ #if defined(__GNUC__)
-       ftolhess=ftol; /* Usually correct */
+ # if defined(__GNUC_PATCHLEVEL__)
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     }
+                             + __GNUC_MINOR__ * 100 \
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+                             + __GNUC_PATCHLEVEL__)
-     printf("# Scales (for hessian or gradient estimation)\n");
+ # else
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
-     for(i=1,jk=1; i <=nlstate; i++){
+                             + __GNUC_MINOR__ * 100)
-       for(j=1; j <=nlstate+ndeath; j++){
+ # endif
-         if (j!=i) {
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-           fprintf(ficres,"%1d%1d",i,j);
+    fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
-           printf("%1d%1d",i,j);
-           fprintf(ficlog,"%1d%1d",i,j);
+    if (uname(&sysInfo) != -1) {
-           for(k=1; k<=ncovmodel;k++){
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-             printf(" %.5e",delti[jk]);
+      fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-             fprintf(ficlog," %.5e",delti[jk]);
+    }
-             fprintf(ficres," %.5e",delti[jk]);
+    else
-             jk++;
+       perror("uname() error");
-           }
+    //#ifndef __INTEL_COMPILER
-           printf("\n");
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
-           fprintf(ficlog,"\n");
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
-           fprintf(ficres,"\n");
+    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
-         }
+ #endif
-       }
+ #endif
-     }
+    //   void main()
-     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)
+ #if defined(_MSC_VER)
-       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");
+    if (IsWow64()){
-     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");
+            printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-     /* # 121 Var(a12)\n\ */
+            fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+    }
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+    else{
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+            printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+            fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\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\ */
+    //      printf("\nPress Enter to continue...");
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+    //      getchar();
+    //   }
-     /* Just to have a covariance matrix which will be more understandable
+ #endif
-        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++){
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
-         for(j=1; j <=nlstate+ndeath; j++){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-           if(j==i) continue;
+   int i, j, k, i1 ;
-           for(k=1; k<=ncovmodel;k++){
+   double ftolpl = 1.e-10;
-             jj++;
+   double age, agebase, agelim;
-             ca[0]= k+'a'-1;ca[1]='\0';
-             if(itimes==1){
+     strcpy(filerespl,"pl");
-               if(mle>=1)
+     strcat(filerespl,fileres);
-                 printf("#%1d%1d%d",i,j,k);
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-             }else{
+     }
-               if(mle>=1)
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-                 printf("%1d%1d%d",i,j,k);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+     pstamp(ficrespl);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-             }
+     fprintf(ficrespl,"#Age ");
-             ll=0;
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-             for(li=1;li <=nlstate; li++){
+     fprintf(ficrespl,"\n");
-               for(lj=1;lj <=nlstate+ndeath; lj++){
-                 if(lj==li) continue;
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
-                 for(lk=1;lk<=ncovmodel;lk++){
-                   ll++;
+     agebase=ageminpar;
-                   if(ll<=jj){
+     agelim=agemaxpar;
-                     cb[0]= lk +'a'-1;cb[1]='\0';
-                     if(ll<jj){
+     i1=pow(2,cptcoveff);
-                       if(itimes==1){
+     if (cptcovn < 1){i1=1;}
-                         if(mle>=1)
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-                       }else{
+         k=k+1;
-                         if(mle>=1)
+         /* to clean */
-                           printf(" %.5e",matcov[jj][ll]);
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+         fprintf(ficrespl,"\n#******");
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+         printf("\n#******");
-                       }
+         fprintf(ficlog,"\n#******");
-                     }else{
+         for(j=1;j<=cptcoveff;j++) {
-                       if(itimes==1){
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                         if(mle>=1)
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+         }
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+         fprintf(ficrespl,"******\n");
-                       }else{
+         printf("******\n");
-                         if(mle>=1)
+         fprintf(ficlog,"******\n");
-                           printf(" %.5e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+         fprintf(ficrespl,"#Age ");
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+         for(j=1;j<=cptcoveff;j++) {
-                       }
+           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                     }
+         }
-                   }
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-                 } /* end lk */
+         fprintf(ficrespl,"\n");
-               } /* end lj */
-             } /* end li */
+         for (age=agebase; age<=agelim; age++){
-             if(mle>=1)
+         /* for (age=agebase; age<=agebase; age++){ */
-               printf("\n");
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-             fprintf(ficlog,"\n");
+           fprintf(ficrespl,"%.0f ",age );
-             fprintf(ficres,"\n");
+           for(j=1;j<=cptcoveff;j++)
-             numlinepar++;
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           } /* end k*/
+           for(i=1; i<=nlstate;i++)
-         } /*end j */
+             fprintf(ficrespl," %.5f", prlim[i][i]);
-       } /* end i */
+           fprintf(ficrespl,"\n");
-     } /* end itimes */
+         } /* Age */
+         /* was end of cptcod */
-     fflush(ficlog);
+     } /* cptcov */
-     fflush(ficres);
+ }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ int hPijx(double *p, int bage, int fage){
-       ungetc(c,ficpar);
+     /*------------- h Pij x at various ages ------------*/
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+   int stepsize;
-       fputs(line,ficparo);
+   int agelim;
-     }
+   int hstepm;
-     ungetc(c,ficpar);
+   int nhstepm;
+   int h, i, i1, j, k;
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+   double agedeb;
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+   double ***p3mat;
-     if (fage <= 2) {
-       bage = ageminpar;
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-       fage = agemaxpar;
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-     }
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
-     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);
+     printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-       ungetc(c,ficpar);
+     /*if (stepm<=24) stepsize=2;*/
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+     agelim=AGESUP;
-       fputs(line,ficparo);
+     hstepm=stepsize*YEARM; /* Every year of age */
-     }
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-     ungetc(c,ficpar);
+     /* hstepm=1;   aff par mois*/
-     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);
+     pstamp(ficrespij);
-     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(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     i1= pow(2,cptcoveff);
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     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);
+       /*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+         k=k+1;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /* for (k=1; k <= (int) pow(2,cptcoveff); k++){*/
-       ungetc(c,ficpar);
+         fprintf(ficrespij,"\n#****** ");
-       fgets(line, MAXLINE, ficpar);
+         for(j=1;j<=cptcoveff;j++)
-       puts(line);
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fputs(line,ficparo);
+         fprintf(ficrespij,"******\n");
-     }
-     ungetc(c,ficpar);
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+           oldm=oldms;savm=savms;
-     fprintf(ficres,"pop_based=%d\n",popbased);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           for(i=1; i<=nlstate;i++)
-       ungetc(c,ficpar);
+             for(j=1; j<=nlstate+ndeath;j++)
-       fgets(line, MAXLINE, ficpar);
+               fprintf(ficrespij," %1d-%1d",i,j);
-       puts(line);
+           fprintf(ficrespij,"\n");
-       fputs(line,ficparo);
+           for (h=0; h<=nhstepm; h++){
-     }
+             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-     ungetc(c,ficpar);
+             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+             for(i=1; i<=nlstate;i++)
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+               for(j=1; j<=nlstate+ndeath;j++)
-     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);
+                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-     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(ficrespij,"\n");
-     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);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* day and month of proj2 are not used but only year anproj2.*/
+           fprintf(ficrespij,"\n");
+         }
+       /*}*/
+     }
-     /*  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);
+ /**************** Main Program *****************/
+ /***********************************************/
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ int main(int argc, char *argv[])
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+ {
+ #ifdef GSL
-    /*------------ free_vector  -------------*/
+   const gsl_multimin_fminimizer_type *T;
-    /*  chdir(path); */
+   size_t iteri = 0, it;
+   int rval = GSL_CONTINUE;
-     free_ivector(wav,1,imx);
+   int status = GSL_SUCCESS;
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+   double ssval;
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+ #endif
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-     free_lvector(num,1,n);
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     free_vector(agedc,1,n);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+   int jj, ll, li, lj, lk;
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   int numlinepar=0; /* Current linenumber of parameter file */
-     fclose(ficparo);
+   int itimes;
-     fclose(ficres);
+   int NDIM=2;
+   int vpopbased=0;
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   char ca[32], cb[32];
+   /*  FILE *fichtm; *//* Html File */
-     strcpy(filerespl,"pl");
+   /* FILE *ficgp;*/ /*Gnuplot File */
-     strcat(filerespl,fileres);
+   struct stat info;
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+   double agedeb;
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     }
+   double fret;
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   double dum; /* Dummy variable */
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   double ***p3mat;
-     pstamp(ficrespl);
+   double ***mobaverage;
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
-     fprintf(ficrespl,"#Age ");
+   char line[MAXLINE];
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     fprintf(ficrespl,"\n");
+   char pathr[MAXLINE], pathimach[MAXLINE];
+   char *tok, *val; /* pathtot */
-     prlim=matrix(1,nlstate,1,nlstate);
+   int firstobs=1, lastobs=10;
+   int c,  h , cpt;
-     agebase=ageminpar;
+   int jl;
-     agelim=agemaxpar;
+   int i1, j1, jk, stepsize;
-     ftolpl=1.e-10;
+   int *tab;
-     i1=cptcoveff;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     if (cptcovn < 1){i1=1;}
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   int agemortsup;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   float  sumlpop=0.;
-         k=k+1;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+   double bage=0, fage=110, age, agelim, agebase;
-         fprintf(ficlog,"\n#******");
+   double ftolpl=FTOL;
-         for(j=1;j<=cptcoveff;j++) {
+   double **prlim;
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   double ***param; /* Matrix of parameters */
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   double  *p;
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   double **matcov; /* Matrix of covariance */
-         }
+   double ***delti3; /* Scale */
-         fprintf(ficrespl,"******\n");
+   double *delti; /* Scale */
-         printf("******\n");
+   double ***eij, ***vareij;
-         fprintf(ficlog,"******\n");
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
-         for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-           fprintf(ficrespl,"%.0f ",age );
+   double **ximort;
-           for(j=1;j<=cptcoveff;j++)
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   int *dcwave;
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+   char z[1]="c";
-           fprintf(ficrespl,"\n");
-         }
+   /*char  *strt;*/
-       }
+   char strtend[80];
-     }
-     fclose(ficrespl);
+ /*   setlocale (LC_ALL, ""); */
-     /*------------- h Pij x at various ages ------------*/
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+ /*   setlocale (LC_CTYPE, ""); */
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+ /*   setlocale (LC_MESSAGES, ""); */
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-     }
+   rstart_time = time(NULL);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+   /*tml = *localtime(&start_time.tm_sec);*/
-     /*if (stepm<=24) stepsize=2;*/
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
-     agelim=AGESUP;
-     hstepm=stepsize*YEARM; /* Every year of age */
+ /*  printf("Localtime (at start)=%s",strstart); */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
-     /* hstepm=1;   aff par mois*/
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-     pstamp(ficrespij);
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ /*   tp.tm_sec = mktime(&tmg); */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ /*   strt=asctime(&tmg); */
-         k=k+1;
+ /*   printf("Time(after) =%s",strstart);  */
-         fprintf(ficrespij,"\n#****** ");
+ /*  (void) time (&time_value);
-         for(j=1;j<=cptcoveff;j++)
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ *  tm = *localtime(&time_value);
-         fprintf(ficrespij,"******\n");
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+ */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   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: ");
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     fgets(pathr,FILENAMELENGTH,stdin);
-           for(i=1; i<=nlstate;i++)
+     i=strlen(pathr);
-             for(j=1; j<=nlstate+ndeath;j++)
+     if(pathr[i-1]=='\n')
-               fprintf(ficrespij," %1d-%1d",i,j);
+       pathr[i-1]='\0';
-           fprintf(ficrespij,"\n");
+     i=strlen(pathr);
-           for (h=0; h<=nhstepm; h++){
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+       pathr[i-1]='\0';
-             for(i=1; i<=nlstate;i++)
+    for (tok = pathr; tok != NULL; ){
-               for(j=1; j<=nlstate+ndeath;j++)
+       printf("Pathr |%s|\n",pathr);
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-             fprintf(ficrespij,"\n");
+       printf("val= |%s| pathr=%s\n",val,pathr);
-           }
+       strcpy (pathtot, val);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       if(pathr[0] == '\0') break; /* Dirty */
-           fprintf(ficrespij,"\n");
+     }
-         }
+   }
-       }
+   else{
-     }
+     strcpy(pathtot,argv[1]);
+   }
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   /*cygwin_split_path(pathtot,path,optionfile);
-     fclose(ficrespij);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for(i=1;i<=AGESUP;i++)
+   /* Split argv[0], imach program to get pathimach */
-       for(j=1;j<=NCOVMAX;j++)
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-         for(k=1;k<=NCOVMAX;k++)
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           probs[i][j][k]=0.;
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
-     /*---------- Forecasting ------------------*/
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-     if(prevfcast==1){
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-       /*    if(stepm ==1){*/
+   chdir(path); /* Can be a relative path */
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     printf("Current directory %s!\n",pathcd);
-       /*      }  */
+   strcpy(command,"mkdir ");
-       /*      else{ */
+   strcat(command,optionfilefiname);
-       /*        erreur=108; */
+   if((outcmd=system(command)) != 0){
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-       /*      } */
+     /* fclose(ficlog); */
-     }
+ /*     exit(1); */
+   }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-     /*---------- Health expectancies and variances ------------*/
+ /*     perror("mkdir"); */
+ /*   } */
-     strcpy(filerest,"t");
-     strcat(filerest,fileres);
+   /*-------- arguments in the command line --------*/
-     if((ficrest=fopen(filerest,"w"))==NULL) {
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+   /* Log file */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   strcat(filelog, optionfilefiname);
-     }
+   strcat(filelog,".log");    /* */
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
-     strcpy(filerese,"e");
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     strcat(filerese,fileres);
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+  path=%s \n\
-     }
+  optionfile=%s\n\
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+  optionfilext=%s\n\
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     strcpy(fileresstde,"stde");
+   syscompilerinfo();
-     strcat(fileresstde,fileres);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   printf("Local time (at start):%s",strstart);
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   fflush(ficlog);
-     }
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   /* */
-     strcpy(filerescve,"cve");
+   strcpy(fileres,"r");
-     strcat(filerescve,fileres);
+   strcat(fileres, optionfilefiname);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+   strcat(fileres,".txt");    /* Other files have txt extension */
-       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);
+   /*---------arguments file --------*/
-     }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     strcpy(fileresv,"v");
+     fflush(ficlog);
-     strcat(fileresv,fileres);
+     /* goto end; */
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     exit(70);
-       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);
+   strcpy(filereso,"o");
+   strcat(filereso,fileres);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     printf("Problem with Output resultfile: %s\n", filereso);
-     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     fflush(ficlog);
-     */
+     goto end;
+   }
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /* Reads comments: lines beginning with '#' */
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   numlinepar=0;
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     ungetc(c,ficpar);
-       }
+     fgets(line, MAXLINE, ficpar);
-     }
+     numlinepar++;
+     fputs(line,stdout);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     fputs(line,ficparo);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     fputs(line,ficlog);
-         k=k+1;
+   }
-         fprintf(ficrest,"\n#****** ");
+   ungetc(c,ficpar);
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-         fprintf(ficrest,"******\n");
+   numlinepar++;
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-         fprintf(ficreseij,"\n#****** ");
+   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(ficresstdeij,"\n#****** ");
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-         fprintf(ficrescveij,"\n#****** ");
+   fflush(ficlog);
-         for(j=1;j<=cptcoveff;j++) {
+   while((c=getc(ficpar))=='#' && c!= EOF){
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     ungetc(c,ficpar);
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fgets(line, MAXLINE, ficpar);
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     numlinepar++;
-         }
+     fputs(line, stdout);
-         fprintf(ficreseij,"******\n");
+     //puts(line);
-         fprintf(ficresstdeij,"******\n");
+     fputs(line,ficparo);
-         fprintf(ficrescveij,"******\n");
+     fputs(line,ficlog);
+   }
-         fprintf(ficresvij,"\n#****** ");
+   ungetc(c,ficpar);
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvij,"******\n");
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-         oldm=oldms;savm=savms;
+      v1+v2*age+v2*v3 makes cptcovn = 3
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+   */
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+   if (strlen(model)>1)
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   else
-         oldm=oldms;savm=savms;
+     ncovmodel=2;
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-         if(popbased==1){
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-         }
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-         pstamp(ficrest);
+     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(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     fflush(stdout);
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+     fclose (ficlog);
-         fprintf(ficrest,"\n");
+     goto end;
+   }
-         epj=vector(1,nlstate+1);
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-         for(age=bage; age <=fage ;age++){
+   delti=delti3[1][1];
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-           if (popbased==1) {
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-             if(mobilav ==0){
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-               for(i=1; i<=nlstate;i++)
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-                 prlim[i][i]=probs[(int)age][i][k];
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-             }else{ /* mobilav */
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-               for(i=1; i<=nlstate;i++)
+     fclose (ficparo);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     fclose (ficlog);
-             }
+     goto end;
-           }
+     exit(0);
+   }
-           fprintf(ficrest," %4.0f",age);
+   else if(mle==-3) {
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-             }
+     matcov=matrix(1,npar,1,npar);
-             epj[nlstate+1] +=epj[j];
+   }
-           }
+   else{
+     /* Read guessed parameters */
-           for(i=1, vepp=0.;i <=nlstate;i++)
+     /* Reads comments: lines beginning with '#' */
-             for(j=1;j <=nlstate;j++)
+     while((c=getc(ficpar))=='#' && c!= EOF){
-               vepp += vareij[i][j][(int)age];
+       ungetc(c,ficpar);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+       fgets(line, MAXLINE, ficpar);
-           for(j=1;j <=nlstate;j++){
+       numlinepar++;
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+       fputs(line,stdout);
-           }
+       fputs(line,ficparo);
-           fprintf(ficrest,"\n");
+       fputs(line,ficlog);
-         }
+     }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     ungetc(c,ficpar);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_vector(epj,1,nlstate+1);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       }
+     for(i=1; i <=nlstate; i++){
-     }
+       j=0;
-     free_vector(weight,1,n);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-     free_imatrix(Tvard,1,15,1,2);
+         if(jj==i) continue;
-     free_imatrix(s,1,maxwav+1,1,n);
+         j++;
-     free_matrix(anint,1,maxwav,1,n);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     free_matrix(mint,1,maxwav,1,n);
+         if ((i1 != i) && (j1 != j)){
-     free_ivector(cod,1,n);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-     free_ivector(tab,1,NCOVMAX);
+ It might be a problem of design; if ncovcol and the model are correct\n \
-     fclose(ficreseij);
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-     fclose(ficresstdeij);
+           exit(1);
-     fclose(ficrescveij);
+         }
-     fclose(ficresvij);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     fclose(ficrest);
+         if(mle==1)
-     fclose(ficpar);
+           printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
-     /*------- Variance of period (stable) prevalence------*/
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
-     strcpy(fileresvpl,"vpl");
+           if(mle==1){
-     strcat(fileresvpl,fileres);
+             printf(" %lf",param[i][j][k]);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+             fprintf(ficlog," %lf",param[i][j][k]);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+           }
-       exit(0);
+           else
-     }
+             fprintf(ficlog," %lf",param[i][j][k]);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+         fscanf(ficpar,"\n");
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         numlinepar++;
-         k=k+1;
+         if(mle==1)
-         fprintf(ficresvpl,"\n#****** ");
+           printf("\n");
-         for(j=1;j<=cptcoveff;j++)
+         fprintf(ficlog,"\n");
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficparo,"\n");
-         fprintf(ficresvpl,"******\n");
+       }
+     }
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+     fflush(ficlog);
-         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     /* Reads scales values */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     p=param[1][1];
-       }
-     }
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     fclose(ficresvpl);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-     /*---------- End : free ----------------*/
+       numlinepar++;
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fputs(line,stdout);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-   }  /* mle==-3 arrives here for freeing */
+     }
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     ungetc(c,ficpar);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     for(i=1; i <=nlstate; i++){
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     free_matrix(covar,0,NCOVMAX,1,n);
+         if ( (i1-i) * (j1-j) != 0){
-     free_matrix(matcov,1,npar,1,npar);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     /*free_vector(delti,1,npar);*/
+           exit(1);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         }
-     free_matrix(agev,1,maxwav,1,imx);
+         printf("%1d%1d",i,j);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     free_ivector(ncodemax,1,8);
+         for(k=1; k<=ncovmodel;k++){
-     free_ivector(Tvar,1,15);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-     free_ivector(Tprod,1,15);
+           printf(" %le",delti3[i][j][k]);
-     free_ivector(Tvaraff,1,15);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     free_ivector(Tage,1,15);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     free_ivector(Tcode,1,100);
+         }
+         fscanf(ficpar,"\n");
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+         numlinepar++;
-     free_imatrix(codtab,1,100,1,10);
+         printf("\n");
-   fflush(fichtm);
+         fprintf(ficparo,"\n");
-   fflush(ficgp);
+         fprintf(ficlog,"\n");
+       }
+     }
-   if((nberr >0) || (nbwarn>0)){
+     fflush(ficlog);
-     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);
+     /* Reads covariance matrix */
-   }else{
+     delti=delti3[1][1];
-     printf("End of Imach\n");
-     fprintf(ficlog,"End of Imach\n");
-   }
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   printf("See log file on %s\n",filelog);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     /* Reads comments: lines beginning with '#' */
-   (void) gettimeofday(&end_time,&tzp);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   tm = *localtime(&end_time.tv_sec);
+       ungetc(c,ficpar);
-   tmg = *gmtime(&end_time.tv_sec);
+       fgets(line, MAXLINE, ficpar);
-   strcpy(strtend,asctime(&tm));
+       numlinepar++;
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+       fputs(line,stdout);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+       fputs(line,ficparo);
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+       fputs(line,ficlog);
+     }
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     ungetc(c,ficpar);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     matcov=matrix(1,npar,1,npar);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+     for(i=1; i <=npar; i++)
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
-   fclose(fichtm);
+     for(i=1; i <=npar; i++){
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+       fscanf(ficpar,"%s",str);
-   fclose(fichtmcov);
+       if(mle==1)
-   fclose(ficgp);
+         printf("%s",str);
-   fclose(ficlog);
+       fprintf(ficlog,"%s",str);
-   /*------ End -----------*/
+       fprintf(ficparo,"%s",str);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
-    printf("Before Current directory %s!\n",pathcd);
+         if(mle==1){
-    if(chdir(pathcd) != 0)
+           printf(" %.5le",matcov[i][j]);
-     printf("Can't move to directory %s!\n",path);
+         }
-   if(getcwd(pathcd,MAXLINE) > 0)
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     printf("Current directory %s!\n",pathcd);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+       }
-   sprintf(plotcmd,"gnuplot");
+       fscanf(ficpar,"\n");
- #ifndef UNIX
+       numlinepar++;
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+       if(mle==1)
- #endif
+         printf("\n");
-   if(!stat(plotcmd,&info)){
+       fprintf(ficlog,"\n");
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       fprintf(ficparo,"\n");
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     }
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     for(i=1; i <=npar; i++)
-     }else
+       for(j=i+1;j<=npar;j++)
-       strcpy(pplotcmd,plotcmd);
+         matcov[i][j]=matcov[j][i];
- #ifdef UNIX
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(mle==1)
-     if(!stat(plotcmd,&info)){
+       printf("\n");
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     fprintf(ficlog,"\n");
-     }else
-       strcpy(pplotcmd,plotcmd);
+     fflush(ficlog);
- #endif
-   }else
+     /*-------- Rewriting parameter file ----------*/
-     strcpy(pplotcmd,plotcmd);
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     strcat(rfileres,".");    /* */
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-   if((outcmd=system(plotcmd)) != 0){
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     printf("\n Problem with gnuplot\n");
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-   }
+     }
-   printf(" Wait...");
+     fprintf(ficres,"#%s\n",version);
-   while (z[0] != 'q') {
+   }    /* End of mle != -3 */
-     /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
-     scanf("%s",z);
+   n= lastobs;
- /*     if (z[0] == 'c') system("./imach"); */
+   num=lvector(1,n);
-     if (z[0] == 'e') {
+   moisnais=vector(1,n);
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+   annais=vector(1,n);
-       system(optionfilehtm);
+   moisdc=vector(1,n);
-     }
+   andc=vector(1,n);
-     else if (z[0] == 'g') system(plotcmd);
+   agedc=vector(1,n);
-     else if (z[0] == 'q') exit(0);
+   cod=ivector(1,n);
-   }
+   weight=vector(1,n);
-   end:
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-   while (z[0] != 'q') {
+   mint=matrix(1,maxwav,1,n);
-     printf("\nType  q for exiting: ");
+   anint=matrix(1,maxwav,1,n);
-     scanf("%s",z);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-   }
+   tab=ivector(1,NCOVMAX);
- }
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
+     goto end;
+   /* Calculation of the number of parameters from char model */
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+   }
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* */
+   wav=ivector(1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* Concatenates waves */
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   ncodemax[1]=1;
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel > 2)
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
+   h=0;
+   /*if (cptcovn > 0) */
+   m=pow(2,cptcoveff);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
+           h++;
+           if (h>m)
+             h=1;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     h     1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     1
+            */
+           codtab[h][k]=j;
+           /*codtab[h][Tvar[k]]=j;*/
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
+         }
+       }
+     }
+   }
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
+   /* for(i=1; i <=m ;i++){
+      for(k=1; k <=cptcovn; k++){
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+      }
+      printf("\n");
+      }
+      scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
+   }
+   /*  fclose(ficgp);*/
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
+   }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ \n\
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   fflush(fichtm);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   fprintf(fichtm,"\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+     cens=ivector(1,n);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           break;
+         }
+     }
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
+         j=wav[i];
+         agecens[i]=1.;
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
+           cens[i]= 1;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
+       else cens[i]=-1;
+     }
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     /*printf("%lf %lf", p[1], p[2]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #else
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #else
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
+     prlim=matrix(1,nlstate,1,nlstate);
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar);
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           oldm=oldms;savm=savms; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f",age);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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

Removed from v.1.125
changed lines
	Added in v.1.182