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Diff for /imach/src/imach.c between versions 1.125 and 1.166

-version 1.125, 2006/04/04 15:20:31
+version 1.166, 2014/12/22 11:40:47
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+   Revision 1.142  2014/01/26 03:57:36  brouard
+   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.141  2014/01/26 02:42:01  brouard
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   Revision 1.140  2011/09/02 10:37:54  brouard
+   Summary: times.h is ok with mingw32 now.
+   Revision 1.139  2010/06/14 07:50:17  brouard
+   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+   Revision 1.138  2010/04/30 18:19:40  brouard
+   *** empty log message ***
+   Revision 1.137  2010/04/29 18:11:38  brouard
+   (Module): Checking covariates for more complex models
+   than V1+V2. A lot of change to be done. Unstable.
+   Revision 1.136  2010/04/26 20:30:53  brouard
+   (Module): merging some libgsl code. Fixing computation
+   of likelione (using inter/intrapolation if mle = 0) in order to
+   get same likelihood as if mle=1.
+   Some cleaning of code and comments added.
+   Revision 1.135  2009/10/29 15:33:14  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.134  2009/10/29 13:18:53  brouard
+   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+   Revision 1.133  2009/07/06 10:21:25  brouard
+   just nforces
+   Revision 1.132  2009/07/06 08:22:05  brouard
+   Many tings
+   Revision 1.131  2009/06/20 16:22:47  brouard
+   Some dimensions resccaled
+   Revision 1.130  2009/05/26 06:44:34  brouard
+   (Module): Max Covariate is now set to 20 instead of 8. A
+   lot of cleaning with variables initialized to 0. Trying to make
+   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+   Revision 1.129  2007/08/31 13:49:27  lievre
+   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+   Revision 1.128  2006/06/30 13:02:05  brouard
+   (Module): Clarifications on computing e.j
+   Revision 1.127  2006/04/28 18:11:50  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   (Module): In order to speed up (in case of numerous covariates) we
+   compute health expectancies (without variances) in a first step
+   and then all the health expectancies with variances or standard
+   deviation (needs data from the Hessian matrices) which slows the
+   computation.
+   In the future we should be able to stop the program is only health
+   expectancies and graph are needed without standard deviations.
+   Revision 1.126  2006/04/28 17:23:28  brouard
+   (Module): Yes the sum of survivors was wrong since
+   imach-114 because nhstepm was no more computed in the age
+   loop. Now we define nhstepma in the age loop.
+   Version 0.98h
    Revision 1.125  2006/04/04 15:20:31  lievre
    Errors in calculation of health expectancies. Age was not initialized.
    Forecasting file added.
    Revision 1.124  2006/03/22 17:13:53  lievre
    Parameters are printed with %lf instead of %f (more numbers after the comma).
    The log-likelihood is printed in the log file
    Revision 1.123  2006/03/20 10:52:43  brouard
    * imach.c (Module): <title> changed, corresponds to .htm file
    name. <head> headers where missing.
    * imach.c (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.122  2006/03/20 09:45:41  brouard
    (Module): Weights can have a decimal point as for
    English (a comma might work with a correct LC_NUMERIC environment,
    otherwise the weight is truncated).
    Modification of warning when the covariates values are not 0 or
 .
    Version 0.98g
    Revision 1.121  2006/03/16 17:45:01  lievre
    * imach.c (Module): Comments concerning covariates added
    * imach.c (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.120  2006/03/16 15:10:38  lievre
    (Module): refinements in the computation of lli if
    status=-2 in order to have more reliable computation if stepm is
    not 1 month. Version 0.98f
    Revision 1.119  2006/03/15 17:42:26  brouard
    (Module): Bug if status = -2, the loglikelihood was
    computed as likelihood omitting the logarithm. Version O.98e
    Revision 1.118  2006/03/14 18:20:07  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.117  2006/03/14 17:16:22  brouard
    (Module): varevsij Comments added explaining the second
    table of variances if popbased=1 .
    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    (Module): Function pstamp added
    (Module): Version 0.98d
    Revision 1.116  2006/03/06 10:29:27  brouard
    (Module): Variance-covariance wrong links and
    varian-covariance of ej. is needed (Saito).
    Revision 1.115  2006/02/27 12:17:45  brouard
    (Module): One freematrix added in mlikeli! 0.98c
    Revision 1.114  2006/02/26 12:57:58  brouard
    (Module): Some improvements in processing parameter
    filename with strsep.
    Revision 1.113  2006/02/24 14:20:24  brouard
    (Module): Memory leaks checks with valgrind and:
    datafile was not closed, some imatrix were not freed and on matrix
    allocation too.
    Revision 1.112  2006/01/30 09:55:26  brouard
    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    Revision 1.111  2006/01/25 20:38:18  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    (Module): Comments can be added in data file. Missing date values
    can be a simple dot '.'.
    Revision 1.110  2006/01/25 00:51:50  brouard
    (Module): Lots of cleaning and bugs added (Gompertz)
    Revision 1.109  2006/01/24 19:37:15  brouard
    (Module): Comments (lines starting with a #) are allowed in data.
    Revision 1.108  2006/01/19 18:05:42  lievre
    Gnuplot problem appeared...
    To be fixed
    Revision 1.107  2006/01/19 16:20:37  brouard
    Test existence of gnuplot in imach path
    Revision 1.106  2006/01/19 13:24:36  brouard
    Some cleaning and links added in html output
    Revision 1.105  2006/01/05 20:23:19  lievre
    *** empty log message ***
    Revision 1.104  2005/09/30 16:11:43  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    (Module): If the status is missing at the last wave but we know
    that the person is alive, then we can code his/her status as -2
    (instead of missing=-1 in earlier versions) and his/her
    contributions to the likelihood is 1 - Prob of dying from last
    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    the healthy state at last known wave). Version is 0.98
    Revision 1.103  2005/09/30 15:54:49  lievre
    (Module): sump fixed, loop imx fixed, and simplifications.
    Revision 1.102  2004/09/15 17:31:30  brouard
    Add the possibility to read data file including tab characters.
    Revision 1.101  2004/09/15 10:38:38  brouard
    Fix on curr_time
    Revision 1.100  2004/07/12 18:29:06  brouard
    Add version for Mac OS X. Just define UNIX in Makefile
    Revision 1.99  2004/06/05 08:57:40  brouard
    *** empty log message ***
    Revision 1.98  2004/05/16 15:05:56  brouard
    New version 0.97 . First attempt to estimate force of mortality
    directly from the data i.e. without the need of knowing the health
    state at each age, but using a Gompertz model: log u =a + b*age .
    This is the basic analysis of mortality and should be done before any
    other analysis, in order to test if the mortality estimated from the
    cross-longitudinal survey is different from the mortality estimated
    from other sources like vital statistic data.
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
    the slope with 95% confident intervals.
    Current limitations:
    A) Even if you enter covariates, i.e. with the
    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    B) There is no computation of Life Expectancy nor Life Table.
    Revision 1.97  2004/02/20 13:25:42  lievre
    Version 0.96d. Population forecasting command line is (temporarily)
    suppressed.
    Revision 1.96  2003/07/15 15:38:55  brouard
    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs.
    Revision 1.95  2003/07/08 07:54:34  brouard
    * imach.c (Repository):
    (Repository): Using imachwizard code to output a more meaningful covariance
    matrix (cov(a12,c31) instead of numbers.
    Revision 1.94  2003/06/27 13:00:02  brouard
    Just cleaning
    Revision 1.93  2003/06/25 16:33:55  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    (Module): Version 0.96b
    Revision 1.92  2003/06/25 16:30:45  brouard
    (Module): On windows (cygwin) function asctime_r doesn't
    exist so I changed back to asctime which exists.
    Revision 1.91  2003/06/25 15:30:29  brouard
    * imach.c (Repository): Duplicated warning errors corrected.
    (Repository): Elapsed time after each iteration is now output. It
    helps to forecast when convergence will be reached. Elapsed time
    is stamped in powell.  We created a new html file for the graphs
    concerning matrix of covariance. It has extension -cov.htm.
    Revision 1.90  2003/06/24 12:34:15  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
    of the covariance matrix to be input.
    Revision 1.88  2003/06/23 17:54:56  brouard
    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    Revision 1.87  2003/06/18 12:26:01  brouard
    Version 0.96
    Revision 1.86  2003/06/17 20:04:08  brouard
    (Module): Change position of html and gnuplot routines and added
    routine fileappend.
    Revision 1.85  2003/06/17 13:12:43  brouard
    * imach.c (Repository): Check when date of death was earlier that
    current date of interview. It may happen when the death was just
    prior to the death. In this case, dh was negative and likelihood
    was wrong (infinity). We still send an "Error" but patch by
    assuming that the date of death was just one stepm after the
    interview.
    (Repository): Because some people have very long ID (first column)
    we changed int to long in num[] and we added a new lvector for
    memory allocation. But we also truncated to 8 characters (left
    truncation)
    (Repository): No more line truncation errors.
    Revision 1.84  2003/06/13 21:44:43  brouard
    * imach.c (Repository): Replace "freqsummary" at a correct
    place. It differs from routine "prevalence" which may be called
    many times. Probs is memory consuming and must be used with
    parcimony.
    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    Revision 1.83  2003/06/10 13:39:11  lievre
    *** empty log message ***
    Revision 1.82  2003/06/05 15:57:20  brouard
    Add log in  imach.c and  fullversion number is now printed.
  */
  /*
     Interpolated Markov Chain
    Short summary of the programme:
    This program computes Healthy Life Expectancies from
    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    first survey ("cross") where individuals from different ages are
    interviewed on their health status or degree of disability (in the
    case of a health survey which is our main interest) -2- at least a
    second wave of interviews ("longitudinal") which measure each change
    (if any) in individual health status.  Health expectancies are
    computed from the time spent in each health state according to a
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
    probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
    complex model than "constant and age", you should modify the program
    where the markup *Covariates have to be included here again* invites
    you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
    multinomial logistic model, is clear when the delay between waves is not
    identical for each individual. Also, if a individual missed an
    intermediate interview, the information is lost, but taken into
    account using an interpolation or extrapolation.
    hPijx is the probability to be observed in state i at age x+h
    conditional to the observed state i at age x. The delay 'h' can be
    split into an exact number (nh*stepm) of unobserved intermediate
    states. This elementary transition (by month, quarter,
    semester or year) is modelled as a multinomial logistic.  The hPx
    matrix is simply the matrix product of nh*stepm elementary matrices
    and the contribution of each individual to the likelihood is simply
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
    software can be distributed freely for non commercial use. Latest version
    can be accessed at http://euroreves.ined.fr/imach .
    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    **********************************************************************/
  /*
    main
    read parameterfile
    read datafile
    concatwav
    freqsummary
    if (mle >= 1)
      mlikeli
    print results files
    if mle==1
       computes hessian
    read end of parameter file: agemin, agemax, bage, fage, estepm
        begin-prev-date,...
    open gnuplot file
    open html file
-   period (stable) prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
-   forecasting if prevfcast==1 prevforecast call prevalence()
-   health expectancies
+   h Pij x                         | pij_nom  ficrestpij
-   Variance-covariance of DFLE
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
-   prevalence()
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
-    movingaverage()
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
-   varevsij()
-   if popbased==1 varevsij(,popbased)
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
-   total life expectancies
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
-   Variance of period (stable) prevalence
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
-  end
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
- */
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+   forecasting if prevfcast==1 prevforecast call prevalence()
+   health expectancies
+   Variance-covariance of DFLE
- #include <math.h>
+   prevalence()
- #include <stdio.h>
+    movingaverage()
- #include <stdlib.h>
+   varevsij()
- #include <string.h>
+   if popbased==1 varevsij(,popbased)
- #include <unistd.h>
+   total life expectancies
+   Variance of period (stable) prevalence
- #include <limits.h>
+  end
- #include <sys/types.h>
+ */
- #include <sys/stat.h>
- #include <errno.h>
+ #define POWELL /* Instead of NLOPT */
- extern int errno;
+ #include <math.h>
- /* #include <sys/time.h> */
+ #include <stdio.h>
- #include <time.h>
+ #include <stdlib.h>
- #include "timeval.h"
+ #include <string.h>
- /* #include <libintl.h> */
+ #ifdef _WIN32
- /* #define _(String) gettext (String) */
+ #include <io.h>
+ #else
- #define MAXLINE 256
+ #include <unistd.h>
+ #endif
- #define GNUPLOTPROGRAM "gnuplot"
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #include <limits.h>
- #define FILENAMELENGTH 132
+ #include <sys/types.h>
+ #include <sys/stat.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #include <errno.h>
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ /* extern int errno; */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ /* #ifdef LINUX */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ /* #include <time.h> */
+ /* #include "timeval.h" */
- #define NINTERVMAX 8
+ /* #else */
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ /* #include <sys/time.h> */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ /* #endif */
- #define NCOVMAX 8 /* Maximum number of covariates */
- #define MAXN 20000
+ #include <time.h>
- #define YEARM 12. /* Number of months per year */
- #define AGESUP 130
+ #ifdef GSL
- #define AGEBASE 40
+ #include <gsl/gsl_errno.h>
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #include <gsl/gsl_multimin.h>
- #ifdef UNIX
+ #endif
- #define DIRSEPARATOR '/'
- #define CHARSEPARATOR "/"
+ #ifdef NLOPT
- #define ODIRSEPARATOR '\\'
+ #include <nlopt.h>
- #else
+ typedef struct {
- #define DIRSEPARATOR '\\'
+   double (* function)(double [] );
- #define CHARSEPARATOR "\\"
+ } myfunc_data ;
- #define ODIRSEPARATOR '/'
+ #endif
- #endif
+ /* #include <libintl.h> */
- /* $Id$ */
+ /* #define _(String) gettext (String) */
- /* $State$ */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
- char fullversion[]="$Revision$ $Date$";
+ #define GNUPLOTPROGRAM "gnuplot"
- char strstart[80];
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #define FILENAMELENGTH 132
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int npar=NPARMAX;
- int nlstate=2; /* Number of live states */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int ndeath=1; /* Number of dead states */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- int popbased=0;
+ #define NINTERVMAX 8
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- int maxwav; /* Maxim number of waves */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define MAXN 20000
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define YEARM 12. /**< Number of months per year */
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define AGESUP 130
- int mle, weightopt;
+ #define AGEBASE 40
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #ifdef _WIN32
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define DIRSEPARATOR '\\'
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define CHARSEPARATOR "\\"
- double jmean; /* Mean space between 2 waves */
+ #define ODIRSEPARATOR '/'
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #else
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #define DIRSEPARATOR '/'
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define CHARSEPARATOR "/"
- FILE *ficlog, *ficrespow;
+ #define ODIRSEPARATOR '\\'
- int globpr; /* Global variable for printing or not */
+ #endif
- double fretone; /* Only one call to likelihood */
- long ipmx; /* Number of contributions */
+ /* $Id$ */
- double sw; /* Sum of weights */
+ /* $State$ */
- char filerespow[FILENAMELENGTH];
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
- FILE *ficresilk;
+ char fullversion[]="$Revision$ $Date$";
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ char strstart[80];
- FILE *ficresprobmorprev;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- FILE *fichtm, *fichtmcov; /* Html File */
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- FILE *ficreseij;
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char filerese[FILENAMELENGTH];
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- FILE *ficresstdeij;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- char fileresstde[FILENAMELENGTH];
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- FILE *ficrescveij;
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char filerescve[FILENAMELENGTH];
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- FILE  *ficresvij;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char fileresv[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- FILE  *ficresvpl;
+ int cptcov=0; /* Working variable */
- char fileresvpl[FILENAMELENGTH];
+ int npar=NPARMAX;
- char title[MAXLINE];
+ int nlstate=2; /* Number of live states */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int popbased=0;
- char command[FILENAMELENGTH];
- int  outcmd=0;
+ int *wav; /* Number of waves for this individuual 0 is possible */
+ int maxwav=0; /* Maxim number of waves */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- char filerest[FILENAMELENGTH];
+                    to the likelihood and the sum of weights (done by funcone)*/
- char fileregp[FILENAMELENGTH];
+ int mle=1, weightopt=0;
- char popfile[FILENAMELENGTH];
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ int countcallfunc=0;  /* Count the number of calls to func */
- struct timezone tzp;
+ double jmean=1; /* Mean space between 2 waves */
- extern int gettimeofday();
+ double **matprod2(); /* test */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- long time_value;
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- extern long time();
+ /*FILE *fic ; */ /* Used in readdata only */
- char strcurr[80], strfor[80];
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficlog, *ficrespow;
- char *endptr;
+ int globpr=0; /* Global variable for printing or not */
- long lval;
+ double fretone; /* Only one call to likelihood */
- double dval;
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- #define NR_END 1
+ char filerespow[FILENAMELENGTH];
- #define FREE_ARG char*
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- #define FTOL 1.0e-10
+ FILE *ficresilk;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define NRANSI
+ FILE *ficresprobmorprev;
- #define ITMAX 200
+ FILE *fichtm, *fichtmcov; /* Html File */
+ FILE *ficreseij;
- #define TOL 2.0e-4
+ char filerese[FILENAMELENGTH];
+ FILE *ficresstdeij;
- #define CGOLD 0.3819660
+ char fileresstde[FILENAMELENGTH];
- #define ZEPS 1.0e-10
+ FILE *ficrescveij;
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ char filerescve[FILENAMELENGTH];
+ FILE  *ficresvij;
- #define GOLD 1.618034
+ char fileresv[FILENAMELENGTH];
- #define GLIMIT 100.0
+ FILE  *ficresvpl;
- #define TINY 1.0e-20
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
- static double maxarg1,maxarg2;
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ int  outcmd=0;
- #define rint(a) floor(a+0.5)
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- static double sqrarg;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ char filelog[FILENAMELENGTH]; /* Log file */
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char filerest[FILENAMELENGTH];
- int agegomp= AGEGOMP;
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
- int imx;
- int stepm=1;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- /* Stepm, step in month: minimum step interpolation*/
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- int estepm;
+ /* struct timezone tzp; */
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ /* extern int gettimeofday(); */
+ struct tm tml, *gmtime(), *localtime();
- int m,nb;
- long *num;
+ extern time_t time();
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- double **pmmij, ***probs;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- double *ageexmed,*agecens;
+ struct tm tm;
- double dateintmean=0;
+ char strcurr[80], strfor[80];
- double *weight;
- int **s; /* Status */
+ char *endptr;
- double *agedc, **covar, idx;
+ long lval;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double dval;
- double *lsurv, *lpop, *tpop;
+ #define NR_END 1
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ #define FREE_ARG char*
- double ftolhess; /* Tolerance for computing hessian */
+ #define FTOL 1.0e-10
- /**************** split *************************/
+ #define NRANSI
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ #define ITMAX 200
- {
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ #define TOL 2.0e-4
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ #define CGOLD 0.3819660
-   char  *ss;                            /* pointer */
+ #define ZEPS 1.0e-10
-   int   l1, l2;                         /* length counters */
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-   l1 = strlen(path );                   /* length of path */
+ #define GOLD 1.618034
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define GLIMIT 100.0
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define TINY 1.0e-20
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ static double maxarg1,maxarg2;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     /* get current working directory */
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define rint(a) floor(a+0.5)
-       return( GLOCK_ERROR_GETCWD );
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
-     }
+ /* #define mytinydouble 1.0e-16 */
-     /* got dirc from getcwd*/
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
-     printf(" DIRC = %s \n",dirc);
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
-   } else {                              /* strip direcotry from path */
+ /* static double dsqrarg; */
-     ss++;                               /* after this, the filename */
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
-     l2 = strlen( ss );                  /* length of filename */
+ static double sqrarg;
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-     strcpy( name, ss );         /* save file name */
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ int agegomp= AGEGOMP;
-     dirc[l1-l2] = 0;                    /* add zero */
-     printf(" DIRC2 = %s \n",dirc);
+ int imx;
-   }
+ int stepm=1;
-   /* We add a separator at the end of dirc if not exists */
+ /* Stepm, step in month: minimum step interpolation*/
-   l1 = strlen( dirc );                  /* length of directory */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ int estepm;
-     dirc[l1] =  DIRSEPARATOR;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     dirc[l1+1] = 0;
-     printf(" DIRC3 = %s \n",dirc);
+ int m,nb;
-   }
+ long *num;
-   ss = strrchr( name, '.' );            /* find last / */
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-   if (ss >0){
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-     ss++;
+ double **pmmij, ***probs;
-     strcpy(ext,ss);                     /* save extension */
+ double *ageexmed,*agecens;
-     l1= strlen( name);
+ double dateintmean=0;
-     l2= strlen(ss)+1;
-     strncpy( finame, name, l1-l2);
+ double *weight;
-     finame[l1-l2]= 0;
+ int **s; /* Status */
-   }
+ double *agedc;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   return( 0 );                          /* we're done */
+                   * covar=matrix(0,NCOVMAX,1,n);
- }
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- /******************************************/
+ int *Ndum; /** Freq of modality (tricode */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
- void replace_back_to_slash(char *s, char*t)
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
- {
+ double *lsurv, *lpop, *tpop;
-   int i;
-   int lg=0;
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-   i=0;
+ double ftolhess; /**< Tolerance for computing hessian */
-   lg=strlen(t);
-   for(i=0; i<= lg; i++) {
+ /**************** split *************************/
-     (s[i] = t[i]);
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-     if (t[i]== '\\') s[i]='/';
+ {
-   }
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
- }
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+   */
- int nbocc(char *s, char occ)
+   char  *ss;                            /* pointer */
- {
+   int   l1, l2;                         /* length counters */
-   int i,j=0;
-   int lg=20;
+   l1 = strlen(path );                   /* length of path */
-   i=0;
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   lg=strlen(s);
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   for(i=0; i<= lg; i++) {
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   if  (s[i] == occ ) j++;
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   }
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   return j;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- }
+     /* get current working directory */
+     /*    extern  char* getcwd ( char *buf , int len);*/
- void cutv(char *u,char *v, char*t, char occ)
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
- {
+       return( GLOCK_ERROR_GETCWD );
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     }
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+     /* got dirc from getcwd*/
-      gives u="abcedf" and v="ghi2j" */
+     printf(" DIRC = %s \n",dirc);
-   int i,lg,j,p=0;
+   } else {                              /* strip direcotry from path */
-   i=0;
+     ss++;                               /* after this, the filename */
-   for(j=0; j<=strlen(t)-1; j++) {
+     l2 = strlen( ss );                  /* length of filename */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   }
+     strcpy( name, ss );         /* save file name */
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   lg=strlen(t);
+     dirc[l1-l2] = 0;                    /* add zero */
-   for(j=0; j<p; j++) {
+     printf(" DIRC2 = %s \n",dirc);
-     (u[j] = t[j]);
+   }
-   }
+   /* We add a separator at the end of dirc if not exists */
-      u[p]='\0';
+   l1 = strlen( dirc );                  /* length of directory */
+   if( dirc[l1-1] != DIRSEPARATOR ){
-    for(j=0; j<= lg; j++) {
+     dirc[l1] =  DIRSEPARATOR;
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     dirc[l1+1] = 0;
-   }
+     printf(" DIRC3 = %s \n",dirc);
- }
+   }
+   ss = strrchr( name, '.' );            /* find last / */
- /********************** nrerror ********************/
+   if (ss >0){
+     ss++;
- void nrerror(char error_text[])
+     strcpy(ext,ss);                     /* save extension */
- {
+     l1= strlen( name);
-   fprintf(stderr,"ERREUR ...\n");
+     l2= strlen(ss)+1;
-   fprintf(stderr,"%s\n",error_text);
+     strncpy( finame, name, l1-l2);
-   exit(EXIT_FAILURE);
+     finame[l1-l2]= 0;
- }
+   }
- /*********************** vector *******************/
- double *vector(int nl, int nh)
+   return( 0 );                          /* we're done */
- {
+ }
-   double *v;
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   if (!v) nrerror("allocation failure in vector");
+ /******************************************/
-   return v-nl+NR_END;
- }
+ void replace_back_to_slash(char *s, char*t)
+ {
- /************************ free vector ******************/
+   int i;
- void free_vector(double*v, int nl, int nh)
+   int lg=0;
- {
+   i=0;
-   free((FREE_ARG)(v+nl-NR_END));
+   lg=strlen(t);
- }
+   for(i=0; i<= lg; i++) {
+     (s[i] = t[i]);
- /************************ivector *******************************/
+     if (t[i]== '\\') s[i]='/';
- int *ivector(long nl,long nh)
+   }
- {
+ }
-   int *v;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ char *trimbb(char *out, char *in)
-   if (!v) nrerror("allocation failure in ivector");
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   return v-nl+NR_END;
+   char *s;
- }
+   s=out;
+   while (*in != '\0'){
- /******************free ivector **************************/
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- void free_ivector(int *v, long nl, long nh)
+       in++;
- {
+     }
-   free((FREE_ARG)(v+nl-NR_END));
+     *out++ = *in++;
- }
+   }
+   *out='\0';
- /************************lvector *******************************/
+   return s;
- long *lvector(long nl,long nh)
+ }
- {
-   long *v;
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ {
-   if (!v) nrerror("allocation failure in ivector");
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
-   return v-nl+NR_END;
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- }
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- /******************free lvector **************************/
+   */
- void free_lvector(long *v, long nl, long nh)
+   char *s, *t;
- {
+   t=in;s=in;
-   free((FREE_ARG)(v+nl-NR_END));
+   while ((*in != occ) && (*in != '\0')){
- }
+     *alocc++ = *in++;
+   }
- /******************* imatrix *******************************/
+   if( *in == occ){
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+     *(alocc)='\0';
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+     s=++in;
- {
+   }
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   int **m;
+   if (s == t) {/* occ not found */
+     *(alocc-(in-s))='\0';
-   /* allocate pointers to rows */
+     in=s;
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   }
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   while ( *in != '\0'){
-   m += NR_END;
+     *blocc++ = *in++;
-   m -= nrl;
+   }
+   *blocc='\0';
-   /* allocate rows and set pointers to them */
+   return t;
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   m[nrl] += NR_END;
+ {
-   m[nrl] -= ncl;
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   /* return pointer to array of pointers to rows */
+   */
-   return m;
+   char *s, *t;
- }
+   t=in;s=in;
+   while (*in != '\0'){
- /****************** free_imatrix *************************/
+     while( *in == occ){
- void free_imatrix(m,nrl,nrh,ncl,nch)
+       *blocc++ = *in++;
-       int **m;
+       s=in;
-       long nch,ncl,nrh,nrl;
+     }
-      /* free an int matrix allocated by imatrix() */
+     *blocc++ = *in++;
- {
+   }
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   if (s == t) /* occ not found */
-   free((FREE_ARG) (m+nrl-NR_END));
+     *(blocc-(in-s))='\0';
- }
+   else
+     *(blocc-(in-s)-1)='\0';
- /******************* matrix *******************************/
+   in=s;
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   while ( *in != '\0'){
- {
+     *alocc++ = *in++;
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   }
-   double **m;
+   *alocc='\0';
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   return s;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ }
-   m += NR_END;
-   m -= nrl;
+ int nbocc(char *s, char occ)
+ {
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   int i,j=0;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   int lg=20;
-   m[nrl] += NR_END;
+   i=0;
-   m[nrl] -= ncl;
+   lg=strlen(s);
+   for(i=0; i<= lg; i++) {
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   if  (s[i] == occ ) j++;
-   return m;
+   }
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+   return j;
-    */
+ }
- }
+ /* void cutv(char *u,char *v, char*t, char occ) */
- /*************************free matrix ************************/
+ /* { */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- {
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   free((FREE_ARG)(m+nrl-NR_END));
+ /*   int i,lg,j,p=0; */
- }
+ /*   i=0; */
+ /*   lg=strlen(t); */
- /******************* ma3x *******************************/
+ /*   for(j=0; j<=lg-1; j++) { */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
- {
+ /*   } */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-   double ***m;
+ /*   for(j=0; j<p; j++) { */
+ /*     (u[j] = t[j]); */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*   } */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*      u[p]='\0'; */
-   m += NR_END;
-   m -= nrl;
+ /*    for(j=0; j<= lg; j++) { */
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   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;
-   m[nrl] -= ncl;
+ #ifdef _WIN32
+ char * strsep(char **pp, const char *delim)
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ {
+   char *p, *q;
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   if ((p = *pp) == NULL)
-   m[nrl][ncl] += NR_END;
+     return 0;
-   m[nrl][ncl] -= nll;
+   if ((q = strpbrk (p, delim)) != NULL)
-   for (j=ncl+1; j<=nch; j++)
+   {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+     *pp = q + 1;
+     *q = '\0';
-   for (i=nrl+1; i<=nrh; i++) {
+   }
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   else
-     for (j=ncl+1; j<=nch; j++)
+     *pp = 0;
-       m[i][j]=m[i][j-1]+nlay;
+   return p;
-   }
+ }
-   return m;
+ #endif
-   /*  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)
+ /********************** nrerror ********************/
-   */
- }
+ void nrerror(char error_text[])
+ {
- /*************************free ma3x ************************/
+   fprintf(stderr,"ERREUR ...\n");
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   fprintf(stderr,"%s\n",error_text);
- {
+   exit(EXIT_FAILURE);
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ }
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ /*********************** vector *******************/
-   free((FREE_ARG)(m+nrl-NR_END));
+ double *vector(int nl, int nh)
- }
+ {
+   double *v;
- /*************** function subdirf ***********/
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
- char *subdirf(char fileres[])
+   if (!v) nrerror("allocation failure in vector");
- {
+   return v-nl+NR_END;
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/"); /* Add to the right */
+ /************************ free vector ******************/
-   strcat(tmpout,fileres);
+ void free_vector(double*v, int nl, int nh)
-   return tmpout;
+ {
- }
+   free((FREE_ARG)(v+nl-NR_END));
+ }
- /*************** function subdirf2 ***********/
- char *subdirf2(char fileres[], char *preop)
+ /************************ivector *******************************/
- {
+ int *ivector(long nl,long nh)
+ {
-   /* Caution optionfilefiname is hidden */
+   int *v;
-   strcpy(tmpout,optionfilefiname);
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   strcat(tmpout,"/");
+   if (!v) nrerror("allocation failure in ivector");
-   strcat(tmpout,preop);
+   return v-nl+NR_END;
-   strcat(tmpout,fileres);
+ }
-   return tmpout;
- }
+ /******************free ivector **************************/
+ void free_ivector(int *v, long nl, long nh)
- /*************** function subdirf3 ***********/
+ {
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   free((FREE_ARG)(v+nl-NR_END));
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /************************lvector *******************************/
-   strcpy(tmpout,optionfilefiname);
+ long *lvector(long nl,long nh)
-   strcat(tmpout,"/");
+ {
-   strcat(tmpout,preop);
+   long *v;
-   strcat(tmpout,preop2);
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   strcat(tmpout,fileres);
+   if (!v) nrerror("allocation failure in ivector");
-   return tmpout;
+   return v-nl+NR_END;
  }
- /***************** f1dim *************************/
+ /******************free lvector **************************/
- extern int ncom;
+ void free_lvector(long *v, long nl, long nh)
- extern double *pcom,*xicom;
+ {
- extern double (*nrfunc)(double []);
+   free((FREE_ARG)(v+nl-NR_END));
+ }
- double f1dim(double x)
- {
+ /******************* imatrix *******************************/
-   int j;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   double f;
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   double *xt;
+ {
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   xt=vector(1,ncom);
+   int **m;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   f=(*nrfunc)(xt);
+   /* allocate pointers to rows */
-   free_vector(xt,1,ncom);
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   return f;
+   if (!m) nrerror("allocation failure 1 in matrix()");
- }
+   m += NR_END;
+   m -= nrl;
- /*****************brent *************************/
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- {
+   /* allocate rows and set pointers to them */
-   int iter;
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   double a,b,d,etemp;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   double fu,fv,fw,fx;
+   m[nrl] += NR_END;
-   double ftemp;
+   m[nrl] -= ncl;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
-   double e=0.0;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   a=(ax < cx ? ax : cx);
+   /* return pointer to array of pointers to rows */
-   b=(ax > cx ? ax : cx);
+   return m;
-   x=w=v=bx;
+ }
-   fw=fv=fx=(*f)(x);
-   for (iter=1;iter<=ITMAX;iter++) {
+ /****************** free_imatrix *************************/
-     xm=0.5*(a+b);
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+       int **m;
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+       long nch,ncl,nrh,nrl;
-     printf(".");fflush(stdout);
+      /* free an int matrix allocated by imatrix() */
-     fprintf(ficlog,".");fflush(ficlog);
+ {
- #ifdef DEBUG
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     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);
+   free((FREE_ARG) (m+nrl-NR_END));
-     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)))) { */
- #endif
+ /******************* matrix *******************************/
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-       *xmin=x;
+ {
-       return fx;
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-     }
+   double **m;
-     ftemp=fu;
-     if (fabs(e) > tol1) {
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       r=(x-w)*(fx-fv);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       q=(x-v)*(fx-fw);
+   m += NR_END;
-       p=(x-v)*q-(x-w)*r;
+   m -= nrl;
-       q=2.0*(q-r);
-       if (q > 0.0) p = -p;
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       q=fabs(q);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       etemp=e;
+   m[nrl] += NR_END;
-       e=d;
+   m[nrl] -= ncl;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-       else {
+   return m;
-         d=p/q;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-         u=x+d;
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-         if (u-a < tol2 || b-u < tol2)
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-           d=SIGN(tol1,xm-x);
+    */
-       }
+ }
-     } else {
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /*************************free matrix ************************/
-     }
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ {
-     fu=(*f)(u);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     if (fu <= fx) {
+   free((FREE_ARG)(m+nrl-NR_END));
-       if (u >= x) a=x; else b=x;
+ }
-       SHFT(v,w,x,u)
-         SHFT(fv,fw,fx,fu)
+ /******************* ma3x *******************************/
-         } else {
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-           if (u < x) a=u; else b=u;
+ {
-           if (fu <= fw || w == x) {
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-             v=w;
+   double ***m;
-             w=u;
-             fv=fw;
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-             fw=fu;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-           } else if (fu <= fv || v == x || v == w) {
+   m += NR_END;
-             v=u;
+   m -= nrl;
-             fv=fu;
-           }
+   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;
-   nrerror("Too many iterations in brent");
+   m[nrl] -= ncl;
-   *xmin=x;
-   return fx;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- }
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
- /****************** mnbrak ***********************/
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   m[nrl][ncl] += NR_END;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   m[nrl][ncl] -= nll;
-             double (*func)(double))
+   for (j=ncl+1; j<=nch; j++)
- {
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   double ulim,u,r,q, dum;
-   double fu;
+   for (i=nrl+1; i<=nrh; i++) {
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   *fa=(*func)(*ax);
+     for (j=ncl+1; j<=nch; j++)
-   *fb=(*func)(*bx);
+       m[i][j]=m[i][j-1]+nlay;
-   if (*fb > *fa) {
+   }
-     SHFT(dum,*ax,*bx,dum)
+   return m;
-       SHFT(dum,*fb,*fa,dum)
+   /*  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)
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   */
-   *fc=(*func)(*cx);
+ }
-   while (*fb > *fc) {
-     r=(*bx-*ax)*(*fb-*fc);
+ /*************************free ma3x ************************/
-     q=(*bx-*cx)*(*fb-*fa);
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+ {
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   free((FREE_ARG)(m+nrl-NR_END));
-       fu=(*func)(u);
+ }
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       fu=(*func)(u);
+ /*************** function subdirf ***********/
-       if (fu < *fc) {
+ char *subdirf(char fileres[])
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ {
-           SHFT(*fb,*fc,fu,(*func)(u))
+   /* Caution optionfilefiname is hidden */
-           }
+   strcpy(tmpout,optionfilefiname);
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   strcat(tmpout,"/"); /* Add to the right */
-       u=ulim;
+   strcat(tmpout,fileres);
-       fu=(*func)(u);
+   return tmpout;
-     } else {
+ }
-       u=(*cx)+GOLD*(*cx-*bx);
-       fu=(*func)(u);
+ /*************** function subdirf2 ***********/
-     }
+ char *subdirf2(char fileres[], char *preop)
-     SHFT(*ax,*bx,*cx,u)
+ {
-       SHFT(*fa,*fb,*fc,fu)
-       }
+   /* Caution optionfilefiname is hidden */
- }
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
- /*************** linmin ************************/
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
- int ncom;
+   return tmpout;
- double *pcom,*xicom;
+ }
- double (*nrfunc)(double []);
+ /*************** function subdirf3 ***********/
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ char *subdirf3(char fileres[], char *preop, char *preop2)
  {
-   double brent(double ax, double bx, double cx,
-                double (*f)(double), double tol, double *xmin);
+   /* Caution optionfilefiname is hidden */
-   double f1dim(double x);
+   strcpy(tmpout,optionfilefiname);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   strcat(tmpout,"/");
-               double *fc, double (*func)(double));
+   strcat(tmpout,preop);
-   int j;
+   strcat(tmpout,preop2);
-   double xx,xmin,bx,ax;
+   strcat(tmpout,fileres);
-   double fx,fb,fa;
+   return tmpout;
+ }
-   ncom=n;
-   pcom=vector(1,n);
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   xicom=vector(1,n);
+ {
-   nrfunc=func;
+   long sec_left, days, hours, minutes;
-   for (j=1;j<=n;j++) {
+   days = (time_sec) / (60*60*24);
-     pcom[j]=p[j];
+   sec_left = (time_sec) % (60*60*24);
-     xicom[j]=xi[j];
+   hours = (sec_left) / (60*60) ;
-   }
+   sec_left = (sec_left) %(60*60);
-   ax=0.0;
+   minutes = (sec_left) /60;
-   xx=1.0;
+   sec_left = (sec_left) % (60);
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   return ascdiff;
- #ifdef DEBUG
+ }
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ /***************** f1dim *************************/
- #endif
+ extern int ncom;
-   for (j=1;j<=n;j++) {
+ extern double *pcom,*xicom;
-     xi[j] *= xmin;
+ extern double (*nrfunc)(double []);
-     p[j] += xi[j];
-   }
+ double f1dim(double x)
-   free_vector(xicom,1,n);
+ {
-   free_vector(pcom,1,n);
+   int j;
- }
+   double f;
+   double *xt;
- char *asc_diff_time(long time_sec, char ascdiff[])
- {
+   xt=vector(1,ncom);
-   long sec_left, days, hours, minutes;
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   days = (time_sec) / (60*60*24);
+   f=(*nrfunc)(xt);
-   sec_left = (time_sec) % (60*60*24);
+   free_vector(xt,1,ncom);
-   hours = (sec_left) / (60*60) ;
+   return f;
-   sec_left = (sec_left) %(60*60);
+ }
-   minutes = (sec_left) /60;
-   sec_left = (sec_left) % (60);
+ /*****************brent *************************/
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-   return ascdiff;
+ {
- }
+   int iter;
+   double a,b,d,etemp;
- /*************** powell ************************/
+   double fu=0,fv,fw,fx;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   double ftemp=0.;
-             double (*func)(double []))
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
- {
+   double e=0.0;
-   void linmin(double p[], double xi[], int n, double *fret,
-               double (*func)(double []));
+   a=(ax < cx ? ax : cx);
-   int i,ibig,j;
+   b=(ax > cx ? ax : cx);
-   double del,t,*pt,*ptt,*xit;
+   x=w=v=bx;
-   double fp,fptt;
+   fw=fv=fx=(*f)(x);
-   double *xits;
+   for (iter=1;iter<=ITMAX;iter++) {
-   int niterf, itmp;
+     xm=0.5*(a+b);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   pt=vector(1,n);
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-   ptt=vector(1,n);
+     printf(".");fflush(stdout);
-   xit=vector(1,n);
+     fprintf(ficlog,".");fflush(ficlog);
-   xits=vector(1,n);
+ #ifdef DEBUGBRENT
-   *fret=(*func)(p);
+     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);
-   for (j=1;j<=n;j++) pt[j]=p[j];
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-   for (*iter=1;;++(*iter)) {
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-     fp=(*fret);
+ #endif
-     ibig=0;
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-     del=0.0;
+       *xmin=x;
-     last_time=curr_time;
+       return fx;
-     (void) gettimeofday(&curr_time,&tzp);
+     }
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+     ftemp=fu;
-     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);
+     if (fabs(e) > tol1) {
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+       r=(x-w)*(fx-fv);
-    for (i=1;i<=n;i++) {
+       q=(x-v)*(fx-fw);
-       printf(" %d %.12f",i, p[i]);
+       p=(x-v)*q-(x-w)*r;
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+       q=2.0*(q-r);
-       fprintf(ficrespow," %.12lf", p[i]);
+       if (q > 0.0) p = -p;
-     }
+       q=fabs(q);
-     printf("\n");
+       etemp=e;
-     fprintf(ficlog,"\n");
+       e=d;
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-     if(*iter <=3){
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       tm = *localtime(&curr_time.tv_sec);
+       else {
-       strcpy(strcurr,asctime(&tm));
+         d=p/q;
- /*       asctime_r(&tm,strcurr); */
+         u=x+d;
-       forecast_time=curr_time;
+         if (u-a < tol2 || b-u < tol2)
-       itmp = strlen(strcurr);
+           d=SIGN(tol1,xm-x);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+       }
-         strcurr[itmp-1]='\0';
+     } else {
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     }
-       for(niterf=10;niterf<=30;niterf+=10){
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+     fu=(*f)(u);
-         tmf = *localtime(&forecast_time.tv_sec);
+     if (fu <= fx) {
- /*      asctime_r(&tmf,strfor); */
+       if (u >= x) a=x; else b=x;
-         strcpy(strfor,asctime(&tmf));
+       SHFT(v,w,x,u)
-         itmp = strlen(strfor);
+         SHFT(fv,fw,fx,fu)
-         if(strfor[itmp-1]=='\n')
+         } else {
-         strfor[itmp-1]='\0';
+           if (u < x) a=u; else b=u;
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+           if (fu <= fw || w == x) {
-         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);
+             v=w;
-       }
+             w=u;
-     }
+             fv=fw;
-     for (i=1;i<=n;i++) {
+             fw=fu;
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+           } else if (fu <= fv || v == x || v == w) {
-       fptt=(*fret);
+             v=u;
- #ifdef DEBUG
+             fv=fu;
-       printf("fret=%lf \n",*fret);
+           }
-       fprintf(ficlog,"fret=%lf \n",*fret);
+         }
- #endif
+   }
-       printf("%d",i);fflush(stdout);
+   nrerror("Too many iterations in brent");
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+   *xmin=x;
-       linmin(p,xit,n,fret,func);
+   return fx;
-       if (fabs(fptt-(*fret)) > del) {
+ }
-         del=fabs(fptt-(*fret));
-         ibig=i;
+ /****************** mnbrak ***********************/
-       }
- #ifdef DEBUG
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-       printf("%d %.12e",i,(*fret));
+             double (*func)(double))
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+ {
-       for (j=1;j<=n;j++) {
+   double ulim,u,r,q, dum;
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   double fu;
-         printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   *fa=(*func)(*ax);
-       }
+   *fb=(*func)(*bx);
-       for(j=1;j<=n;j++) {
+   if (*fb > *fa) {
-         printf(" p=%.12e",p[j]);
+     SHFT(dum,*ax,*bx,dum)
-         fprintf(ficlog," p=%.12e",p[j]);
+       SHFT(dum,*fb,*fa,dum)
        }
-       printf("\n");
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       fprintf(ficlog,"\n");
+   *fc=(*func)(*cx);
- #endif
+   while (*fb > *fc) { /* Declining fa, fb, fc */
-     }
+     r=(*bx-*ax)*(*fb-*fc);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+     q=(*bx-*cx)*(*fb-*fa);
- #ifdef DEBUG
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       int k[2],l;
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-       k[0]=1;
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-       k[1]=-1;
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
-       printf("Max: %.12e",(*func)(p));
+       fu=(*func)(u);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+ #ifdef DEBUG
-       for (j=1;j<=n;j++) {
+       /* f(x)=A(x-u)**2+f(u) */
-         printf(" %.12e",p[j]);
+       double A, fparabu;
-         fprintf(ficlog," %.12e",p[j]);
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-       }
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-       printf("\n");
+       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,"\n");
+       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);
-       for(l=0;l<=1;l++) {
+ #endif
-         for (j=1;j<=n;j++) {
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       fu=(*func)(u);
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       if (fu < *fc) {
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         }
+           SHFT(*fb,*fc,fu,(*func)(u))
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+           }
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-       }
+       u=ulim;
- #endif
+       fu=(*func)(u);
+     } else {
+       u=(*cx)+GOLD*(*cx-*bx);
-       free_vector(xit,1,n);
+       fu=(*func)(u);
-       free_vector(xits,1,n);
+     }
-       free_vector(ptt,1,n);
+     SHFT(*ax,*bx,*cx,u)
-       free_vector(pt,1,n);
+       SHFT(*fa,*fb,*fc,fu)
-       return;
+       }
-     }
+ }
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-     for (j=1;j<=n;j++) {
+ /*************** linmin ************************/
-       ptt[j]=2.0*p[j]-pt[j];
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-       xit[j]=p[j]-pt[j];
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-       pt[j]=p[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
-     fptt=(*func)(ptt);
+ routines mnbrak and brent .*/
-     if (fptt < fp) {
+ int ncom;
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ double *pcom,*xicom;
-       if (t < 0.0) {
+ double (*nrfunc)(double []);
-         linmin(p,xit,n,fret,func);
-         for (j=1;j<=n;j++) {
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-           xi[j][ibig]=xi[j][n];
+ {
-           xi[j][n]=xit[j];
+   double brent(double ax, double bx, double cx,
-         }
+                double (*f)(double), double tol, double *xmin);
- #ifdef DEBUG
+   double f1dim(double x);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+               double *fc, double (*func)(double));
-         for(j=1;j<=n;j++){
+   int j;
-           printf(" %.12e",xit[j]);
+   double xx,xmin,bx,ax;
-           fprintf(ficlog," %.12e",xit[j]);
+   double fx,fb,fa;
-         }
-         printf("\n");
+   ncom=n;
-         fprintf(ficlog,"\n");
+   pcom=vector(1,n);
- #endif
+   xicom=vector(1,n);
-       }
+   nrfunc=func;
-     }
+   for (j=1;j<=n;j++) {
-   }
+     pcom[j]=p[j];
- }
+     xicom[j]=xi[j];
+   }
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   ax=0.0;
+   xx=1.0;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
- {
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+ #ifdef DEBUG
-      matrix by transitions matrix until convergence is reached */
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   int i, ii,j,k;
+ #endif
-   double min, max, maxmin, maxmax,sumnew=0.;
+   for (j=1;j<=n;j++) {
-   double **matprod2();
+     xi[j] *= xmin;
-   double **out, cov[NCOVMAX], **pmij();
+     p[j] += xi[j];
-   double **newm;
+   }
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   free_vector(xicom,1,n);
+   free_vector(pcom,1,n);
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+ }
-     for (j=1;j<=nlstate+ndeath;j++){
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     }
+ /*************** powell ************************/
+ /*
-    cov[1]=1.;
+ Minimization of a function func of n variables. Input consists of an initial starting point
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-     newm=savm;
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-     /* Covariates have to be included here again */
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-      cov[2]=agefin;
+  */
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-       for (k=1; k<=cptcovn;k++) {
+             double (*func)(double []))
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ {
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+   void linmin(double p[], double xi[], int n, double *fret,
-       }
+               double (*func)(double []));
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   int i,ibig,j;
-       for (k=1; k<=cptcovprod;k++)
+   double del,t,*pt,*ptt,*xit;
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   double fp,fptt;
+   double *xits;
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   int niterf, itmp;
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   pt=vector(1,n);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   ptt=vector(1,n);
+   xit=vector(1,n);
-     savm=oldm;
+   xits=vector(1,n);
-     oldm=newm;
+   *fret=(*func)(p);
-     maxmax=0.;
+   for (j=1;j<=n;j++) pt[j]=p[j];
-     for(j=1;j<=nlstate;j++){
+     rcurr_time = time(NULL);
-       min=1.;
+   for (*iter=1;;++(*iter)) {
-       max=0.;
+     fp=(*fret);
-       for(i=1; i<=nlstate; i++) {
+     ibig=0;
-         sumnew=0;
+     del=0.0;
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+     rlast_time=rcurr_time;
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+     /* (void) gettimeofday(&curr_time,&tzp); */
-         max=FMAX(max,prlim[i][j]);
+     rcurr_time = time(NULL);
-         min=FMIN(min,prlim[i][j]);
+     curr_time = *localtime(&rcurr_time);
-       }
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-       maxmin=max-min;
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-       maxmax=FMAX(maxmax,maxmin);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-     }
+    for (i=1;i<=n;i++) {
-     if(maxmax < ftolpl){
+       printf(" %d %.12f",i, p[i]);
-       return prlim;
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-     }
+       fprintf(ficrespow," %.12lf", p[i]);
-   }
+     }
- }
+     printf("\n");
+     fprintf(ficlog,"\n");
- /*************** transition probabilities ***************/
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       tml = *localtime(&rcurr_time);
- {
+       strcpy(strcurr,asctime(&tml));
-   double s1, s2;
+       rforecast_time=rcurr_time;
-   /*double t34;*/
+       itmp = strlen(strcurr);
-   int i,j,j1, nc, ii, jj;
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         strcurr[itmp-1]='\0';
-     for(i=1; i<= nlstate; i++){
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       for(j=1; j<i;j++){
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       for(niterf=10;niterf<=30;niterf+=10){
-           /*s2 += param[i][j][nc]*cov[nc];*/
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+         forecast_time = *localtime(&rforecast_time);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+         strcpy(strfor,asctime(&forecast_time));
-         }
+         itmp = strlen(strfor);
-         ps[i][j]=s2;
+         if(strfor[itmp-1]=='\n')
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+         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(j=i+1; j<=nlstate+ndeath;j++){
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       }
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+     }
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+     for (i=1;i<=n;i++) {
-         }
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-         ps[i][j]=s2;
+       fptt=(*fret);
-       }
+ #ifdef DEBUG
-     }
+           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-     /*ps[3][2]=1;*/
+           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
+ #endif
-     for(i=1; i<= nlstate; i++){
+       printf("%d",i);fflush(stdout);
-       s1=0;
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-       for(j=1; j<i; j++)
+       linmin(p,xit,n,fret,func);
-         s1+=exp(ps[i][j]);
+       if (fabs(fptt-(*fret)) > del) {
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         del=fabs(fptt-(*fret));
-         s1+=exp(ps[i][j]);
+         ibig=i;
-       ps[i][i]=1./(s1+1.);
+       }
-       for(j=1; j<i; j++)
+ #ifdef DEBUG
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       printf("%d %.12e",i,(*fret));
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       for (j=1;j<=n;j++) {
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-     } /* end i */
+         printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       for(j=1;j<=n;j++) {
-         ps[ii][jj]=0;
+         printf(" p(%d)=%.12e",j,p[j]);
-         ps[ii][ii]=1;
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
        }
-     }
+       printf("\n");
+       fprintf(ficlog,"\n");
+ #endif
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     } /* end i */
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- /*         printf("ddd %lf ",ps[ii][jj]); */
+ #ifdef DEBUG
- /*       } */
+       int k[2],l;
- /*       printf("\n "); */
+       k[0]=1;
- /*        } */
+       k[1]=-1;
- /*        printf("\n ");printf("%lf ",cov[2]); */
+       printf("Max: %.12e",(*func)(p));
-        /*
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       for (j=1;j<=n;j++) {
-       goto end;*/
+         printf(" %.12e",p[j]);
-     return ps;
+         fprintf(ficlog," %.12e",p[j]);
- }
+       }
+       printf("\n");
- /**************** Product of 2 matrices ******************/
+       fprintf(ficlog,"\n");
+       for(l=0;l<=1;l++) {
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+         for (j=1;j<=n;j++) {
- {
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   /* in, b, out are matrice of pointers which should have been initialized
+         }
-      before: only the contents of out is modified. The function returns
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-      a pointer to pointers identical to out */
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   long i, j, k;
+       }
-   for(i=nrl; i<= nrh; i++)
+ #endif
-     for(k=ncolol; k<=ncoloh; k++)
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
-         out[i][k] +=in[i][j]*b[j][k];
+       free_vector(xit,1,n);
+       free_vector(xits,1,n);
-   return out;
+       free_vector(ptt,1,n);
- }
+       free_vector(pt,1,n);
+       return;
+     }
- /************* Higher Matrix Product ***************/
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       ptt[j]=2.0*p[j]-pt[j];
- {
+       xit[j]=p[j]-pt[j];
-   /* Computes the transition matrix starting at age 'age' over
+       pt[j]=p[j];
-      'nhstepm*hstepm*stepm' months (i.e. until
+     }
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+     fptt=(*func)(ptt);
-      nhstepm*hstepm matrices.
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-      (typically every 2 years instead of every month which is too big
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-      for the memory).
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-      Model is determined by parameters x and covariates have to be
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-      included manually here.
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
-      */
+       /* Thus we compare delta(2h) with observed f1-f3 */
+       /* or best gain on one ancient line 'del' with total  */
-   int i, j, d, h, k;
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
-   double **out, cov[NCOVMAX];
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-   double **newm;
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-   /* Hstepm could be zero and should return the unit matrix */
+       t= t- del*SQR(fp-fptt);
-   for (i=1;i<=nlstate+ndeath;i++)
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-     for (j=1;j<=nlstate+ndeath;j++){
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+ #ifdef DEBUG
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       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));
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   for(h=1; h <=nhstepm; h++){
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-     for(d=1; d <=hstepm; d++){
+       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);
-       newm=savm;
+       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);
-       /* Covariates have to be included here again */
+ #endif
-       cov[1]=1.;
+       if (t < 0.0) { /* Then we use it for last direction */
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+         for (j=1;j<=n;j++) {
-       for (k=1; k<=cptcovage;k++)
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
-       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]]];
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+ #ifdef DEBUG
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+         for(j=1;j<=n;j++){
-       savm=oldm;
+           printf(" %.12e",xit[j]);
-       oldm=newm;
+           fprintf(ficlog," %.12e",xit[j]);
-     }
+         }
-     for(i=1; i<=nlstate+ndeath; i++)
+         printf("\n");
-       for(j=1;j<=nlstate+ndeath;j++) {
+         fprintf(ficlog,"\n");
-         po[i][j][h]=newm[i][j];
+ #endif
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+       } /* end of t negative */
-          */
+     } /* end if (fptt < fp)  */
-       }
+   }
-   } /* end h */
+ }
-   return po;
- }
+ /**** Prevalence limit (stable or period prevalence)  ****************/
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
- /*************** log-likelihood *************/
+ {
- double func( double *x)
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
- {
+      matrix by transitions matrix until convergence is reached */
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   int i, ii,j,k;
-   double **out;
+   double min, max, maxmin, maxmax,sumnew=0.;
-   double sw; /* Sum of weights */
+   /* double **matprod2(); */ /* test */
-   double lli; /* Individual log likelihood */
+   double **out, cov[NCOVMAX+1], **pmij();
-   int s1, s2;
+   double **newm;
-   double bbh, survp;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   long ipmx;
-   /*extern weight */
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-   /* We are differentiating ll according to initial status */
+     for (j=1;j<=nlstate+ndeath;j++){
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /*for(i=1;i<imx;i++)
+     }
-     printf(" %d\n",s[4][i]);
-   */
+    cov[1]=1.;
-   cov[1]=1.;
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     newm=savm;
-   if(mle==1){
+     /* Covariates have to be included here again */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     cov[2]=agefin;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     for (k=1; k<=cptcovn;k++) {
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           for (j=1;j<=nlstate+ndeath;j++){
+       /*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]]);*/
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           }
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-         for(d=0; d<dh[mi][i]; d++){
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-           }
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-           savm=oldm;
-           oldm=newm;
+     savm=oldm;
-         } /* end mult */
+     oldm=newm;
+     maxmax=0.;
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     for(j=1;j<=nlstate;j++){
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       min=1.;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+       max=0.;
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       for(i=1; i<=nlstate; i++) {
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+         sumnew=0;
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-          * probability in order to take into account the bias as a fraction of the way
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+         max=FMAX(max,prlim[i][j]);
-          * -stepm/2 to stepm/2 .
+         min=FMIN(min,prlim[i][j]);
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       }
-          * For stepm > 1 the results are less biased than in previous versions.
+       maxmin=max-min;
-          */
+       maxmax=FMAX(maxmax,maxmin);
-         s1=s[mw[mi][i]][i];
+     }
-         s2=s[mw[mi+1][i]][i];
+     if(maxmax < ftolpl){
-         bbh=(double)bh[mi][i]/(double)stepm;
+       return prlim;
-         /* bias bh is positive if real duration
+     }
-          * is higher than the multiple of stepm and negative otherwise.
+   }
-          */
+ }
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-         if( s2 > nlstate){
+ /*************** transition probabilities ***************/
-           /* 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
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-              die between last step unit time and current  step unit time,
+ {
-              which is also equal to probability to die before dh
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-              minus probability to die before dh-stepm .
+      computes the probability to be observed in state j being in state i by appying the
-              In version up to 0.92 likelihood was computed
+      model to the ncovmodel covariates (including constant and age).
-         as if date of death was unknown. Death was treated as any other
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         health state: the date of the interview describes the actual state
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         and not the date of a change in health state. The former idea was
+      ncth covariate in the global vector x is given by the formula:
-         to consider that at each interview the state was recorded
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-         (healthy, disable or death) and IMaCh was corrected; but when we
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-         introduced the exact date of death then we should have modified
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         the contribution of an exact death to the likelihood. This new
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         contribution is smaller and very dependent of the step unit
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-         stepm. It is no more the probability to die between last interview
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         and month of death but the probability to survive from last
+   */
-         interview up to one month before death multiplied by the
+   double s1, lnpijopii;
-         probability to die within a month. Thanks to Chris
+   /*double t34;*/
-         Jackson for correcting this bug.  Former versions increased
+   int i,j, nc, ii, jj;
-         mortality artificially. The bad side is that we add another loop
-         which slows down the processing. The difference can be up to 10%
+     for(i=1; i<= nlstate; i++){
-         lower mortality.
+       for(j=1; j<i;j++){
-           */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           lli=log(out[s1][s2] - savm[s1][s2]);
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         } else if  (s2==-2) {
+         }
-           for (j=1,survp=0. ; j<=nlstate; j++)
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-           /*survp += out[s1][j]; */
+       }
-           lli= log(survp);
+       for(j=i+1; j<=nlstate+ndeath;j++){
-         }
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-         else if  (s2==-4) {
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-           for (j=3,survp=0. ; j<=nlstate; j++)
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         }
-           lli= log(survp);
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         }
+       }
+     }
-         else if  (s2==-5) {
-           for (j=1,survp=0. ; j<=2; j++)
+     for(i=1; i<= nlstate; i++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       s1=0;
-           lli= log(survp);
+       for(j=1; j<i; j++){
-         }
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         else{
+       }
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       for(j=i+1; j<=nlstate+ndeath; j++){
-           /*  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 */
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         }
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       }
-         /*if(lli ==000.0)*/
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         /*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][i]=1./(s1+1.);
-         ipmx +=1;
+       /* Computing other pijs */
-         sw += weight[i];
+       for(j=1; j<i; j++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       } /* end of wave */
+       for(j=i+1; j<=nlstate+ndeath; j++)
-     } /* end of individual */
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-   }  else if(mle==2){
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     } /* end i */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-           for (j=1;j<=nlstate+ndeath;j++){
+         ps[ii][jj]=0;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         ps[ii][ii]=1;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       }
-           }
+     }
-         for(d=0; d<=dh[mi][i]; d++){
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-           for (kk=1; kk<=cptcovage;kk++) {
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-           }
+     /*   } */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     /*   printf("\n "); */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     /* } */
-           savm=oldm;
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-           oldm=newm;
+     /*
-         } /* end mult */
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       goto end;*/
-         s1=s[mw[mi][i]][i];
+     return ps;
-         s2=s[mw[mi+1][i]][i];
+ }
-         bbh=(double)bh[mi][i]/(double)stepm;
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+ /**************** Product of 2 matrices ******************/
-         ipmx +=1;
-         sw += weight[i];
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ {
-       } /* end of wave */
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-     } /* end of individual */
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+   /* in, b, out are matrice of pointers which should have been initialized
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+      before: only the contents of out is modified. The function returns
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      a pointer to pointers identical to out */
-       for(mi=1; mi<= wav[i]-1; mi++){
+   int i, j, k;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   for(i=nrl; i<= nrh; i++)
-           for (j=1;j<=nlstate+ndeath;j++){
+     for(k=ncolol; k<=ncoloh; k++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       out[i][k]=0.;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(j=ncl; j<=nch; j++)
-           }
+         out[i][k] +=in[i][j]*b[j][k];
-         for(d=0; d<dh[mi][i]; d++){
+     }
-           newm=savm;
+   return out;
-           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];
-           }
+ /************* Higher Matrix Product ***************/
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-           savm=oldm;
+ {
-           oldm=newm;
+   /* Computes the transition matrix starting at age 'age' over
-         } /* end mult */
+      'nhstepm*hstepm*stepm' months (i.e. until
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-         s1=s[mw[mi][i]][i];
+      nhstepm*hstepm matrices.
-         s2=s[mw[mi+1][i]][i];
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-         bbh=(double)bh[mi][i]/(double)stepm;
+      (typically every 2 years instead of every month which is too big
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+      for the memory).
-         ipmx +=1;
+      Model is determined by parameters x and covariates have to be
-         sw += weight[i];
+      included manually here.
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       } /* end of wave */
+      */
-     } /* end of individual */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+   int i, j, d, h, k;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   double **out, cov[NCOVMAX+1];
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   double **newm;
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* Hstepm could be zero and should return the unit matrix */
-           for (j=1;j<=nlstate+ndeath;j++){
+   for (i=1;i<=nlstate+ndeath;i++)
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for (j=1;j<=nlstate+ndeath;j++){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-           }
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         for(d=0; d<dh[mi][i]; d++){
+     }
-           newm=savm;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   for(h=1; h <=nhstepm; h++){
-           for (kk=1; kk<=cptcovage;kk++) {
+     for(d=1; d <=hstepm; d++){
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       newm=savm;
-           }
+       /* Covariates have to be included here again */
+       cov[1]=1.;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for (k=1; k<=cptcovn;k++)
-           savm=oldm;
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           oldm=newm;
+       for (k=1; k<=cptcovage;k++)
-         } /* end mult */
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-         s1=s[mw[mi][i]][i];
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         s2=s[mw[mi+1][i]][i];
-         if( s2 > nlstate){
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-         }else{
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-         }
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-         ipmx +=1;
+       savm=oldm;
-         sw += weight[i];
+       oldm=newm;
-         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]); */
+     for(i=1; i<=nlstate+ndeath; i++)
-       } /* end of wave */
+       for(j=1;j<=nlstate+ndeath;j++) {
-     } /* end of individual */
+         po[i][j][h]=newm[i][j];
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     /*printf("h=%d ",h);*/
-       for(mi=1; mi<= wav[i]-1; mi++){
+   } /* end h */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+ /*     printf("\n H=%d \n",h); */
-           for (j=1;j<=nlstate+ndeath;j++){
+   return po;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           }
+ #ifdef NLOPT
-         for(d=0; d<dh[mi][i]; d++){
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-           newm=savm;
+   double fret;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   double *xt;
-           for (kk=1; kk<=cptcovage;kk++) {
+   int j;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   myfunc_data *d2 = (myfunc_data *) pd;
-           }
+ /* xt = (p1-1); */
+   xt=vector(1,n);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-           oldm=newm;
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-         } /* end mult */
+   printf("Function = %.12lf ",fret);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-         s1=s[mw[mi][i]][i];
+   printf("\n");
-         s2=s[mw[mi+1][i]][i];
+  free_vector(xt,1,n);
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+   return fret;
-         ipmx +=1;
+ }
-         sw += weight[i];
+ #endif
-         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]);*/
+ /*************** log-likelihood *************/
-       } /* end of wave */
+ double func( double *x)
-     } /* end of individual */
+ {
-   } /* End of if */
+   int i, ii, j, k, mi, d, kk;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   double **out;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   double sw; /* Sum of weights */
-   return -l;
+   double lli; /* Individual log likelihood */
- }
+   int s1, s2;
+   double bbh, survp;
- /*************** log-likelihood *************/
+   long ipmx;
- double funcone( double *x)
+   /*extern weight */
- {
+   /* We are differentiating ll according to initial status */
-   /* Same as likeli but slower because of a lot of printf and if */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   int i, ii, j, k, mi, d, kk;
+   /*for(i=1;i<imx;i++)
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+     printf(" %d\n",s[4][i]);
-   double **out;
+   */
-   double lli; /* Individual log likelihood */
-   double llt;
+   ++countcallfunc;
-   int s1, s2;
-   double bbh, survp;
+   cov[1]=1.;
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*for(i=1;i<imx;i++)
+   if(mle==1){
-     printf(" %d\n",s[4][i]);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   */
+       /* Computes the values of the ncovmodel covariates of the model
-   cov[1]=1.;
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+          to be observed in j being in i according to the model.
+        */
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         cov[2+k]=covar[Tvar[k]][i];
-     for(mi=1; mi<= wav[i]-1; mi++){
+       }
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-         for (j=1;j<=nlstate+ndeath;j++){
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+          has been calculated etc */
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(mi=1; mi<= wav[i]-1; mi++){
-         }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       for(d=0; d<dh[mi][i]; d++){
+           for (j=1;j<=nlstate+ndeath;j++){
-         newm=savm;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for (kk=1; kk<=cptcovage;kk++) {
+           }
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         for(d=0; d<dh[mi][i]; d++){
-         }
+           newm=savm;
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           for (kk=1; kk<=cptcovage;kk++) {
-         savm=oldm;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-         oldm=newm;
+           }
-       } /* end mult */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       s1=s[mw[mi][i]][i];
+           savm=oldm;
-       s2=s[mw[mi+1][i]][i];
+           oldm=newm;
-       bbh=(double)bh[mi][i]/(double)stepm;
+         } /* end mult */
-       /* bias is positive if real duration
-        * is higher than the multiple of stepm and negative otherwise.
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-        */
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         lli=log(out[s1][s2] - savm[s1][s2]);
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-       } else if  (s2==-2) {
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-         for (j=1,survp=0. ; j<=nlstate; j++)
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         lli= log(survp);
+          * probability in order to take into account the bias as a fraction of the way
-       }else if (mle==1){
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+          * -stepm/2 to stepm/2 .
-       } else if(mle==2){
+          * For stepm=1 the results are the same as for previous versions of Imach.
-         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 stepm > 1 the results are less biased than in previous versions.
-       } else if(mle==3){  /* exponential inter-extrapolation */
+          */
-         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 */
+         s1=s[mw[mi][i]][i];
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         s2=s[mw[mi+1][i]][i];
-         lli=log(out[s1][s2]); /* Original formula */
+         bbh=(double)bh[mi][i]/(double)stepm;
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         /* bias bh is positive if real duration
-         lli=log(out[s1][s2]); /* Original formula */
+          * is higher than the multiple of stepm and negative otherwise.
-       } /* End of if */
+          */
-       ipmx +=1;
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-       sw += weight[i];
+         if( s2 > nlstate){
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           /* i.e. if s2 is a death state and if the date of death is known
- /*       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]); */
+              then the contribution to the likelihood is the probability to
-       if(globpr){
+              die between last step unit time and current  step unit time,
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+              which is also equal to probability to die before dh
-  %11.6f %11.6f %11.6f ", \
+              minus probability to die before dh-stepm .
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+              In version up to 0.92 likelihood was computed
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         as if date of death was unknown. Death was treated as any other
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         health state: the date of the interview describes the actual state
-           llt +=ll[k]*gipmx/gsw;
+         and not the date of a change in health state. The former idea was
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         to consider that at each interview the state was recorded
-         }
+         (healthy, disable or death) and IMaCh was corrected; but when we
-         fprintf(ficresilk," %10.6f\n", -llt);
+         introduced the exact date of death then we should have modified
-       }
+         the contribution of an exact death to the likelihood. This new
-     } /* end of wave */
+         contribution is smaller and very dependent of the step unit
-   } /* end of individual */
+         stepm. It is no more the probability to die between last interview
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         and month of death but the probability to survive from last
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+         interview up to one month before death multiplied by the
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         probability to die within a month. Thanks to Chris
-   if(globpr==0){ /* First time we count the contributions and weights */
+         Jackson for correcting this bug.  Former versions increased
-     gipmx=ipmx;
+         mortality artificially. The bad side is that we add another loop
-     gsw=sw;
+         which slows down the processing. The difference can be up to 10%
-   }
+         lower mortality.
-   return -l;
+           */
- }
+           lli=log(out[s1][s2] - savm[s1][s2]);
- /*************** function likelione ***********/
+         } else if  (s2==-2) {
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+           for (j=1,survp=0. ; j<=nlstate; j++)
- {
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   /* This routine should help understanding what is done with
+           /*survp += out[s1][j]; */
-      the selection of individuals/waves and
+           lli= log(survp);
-      to check the exact contribution to the likelihood.
+         }
-      Plotting could be done.
-    */
+         else if  (s2==-4) {
-   int k;
+           for (j=3,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+           lli= log(survp);
-     strcpy(fileresilk,"ilk");
+         }
-     strcat(fileresilk,fileres);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+         else if  (s2==-5) {
-       printf("Problem with resultfile: %s\n", fileresilk);
+           for (j=1,survp=0. ; j<=2; j++)
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     }
+           lli= log(survp);
-     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");
+         }
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+         else{
-     for(k=1; k<=nlstate; k++)
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         }
-   }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         /*if(lli ==000.0)*/
-   *fretone=(*funcone)(p);
+         /*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); */
-   if(*globpri !=0){
+         ipmx +=1;
-     fclose(ficresilk);
+         sw += weight[i];
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fflush(fichtm);
+       } /* end of wave */
-   }
+     } /* end of individual */
-   return;
+   }  else if(mle==2){
- }
+     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++){
- /*********** Maximum Likelihood Estimation ***************/
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- {
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int i,j, iter;
+           }
-   double **xi;
+         for(d=0; d<=dh[mi][i]; d++){
-   double fret;
+           newm=savm;
-   double fretone; /* Only one call to likelihood */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   /*  char filerespow[FILENAMELENGTH];*/
+           for (kk=1; kk<=cptcovage;kk++) {
-   xi=matrix(1,npar,1,npar);
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   for (i=1;i<=npar;i++)
+           }
-     for (j=1;j<=npar;j++)
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+           savm=oldm;
-   strcpy(filerespow,"pow");
+           oldm=newm;
-   strcat(filerespow,fileres);
+         } /* end mult */
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", filerespow);
+         s1=s[mw[mi][i]][i];
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         s2=s[mw[mi+1][i]][i];
-   }
+         bbh=(double)bh[mi][i]/(double)stepm;
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   for (i=1;i<=nlstate;i++)
+         ipmx +=1;
-     for(j=1;j<=nlstate+ndeath;j++)
+         sw += weight[i];
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   fprintf(ficrespow,"\n");
+       } /* end of wave */
+     } /* end of individual */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+   }  else if(mle==3){  /* exponential inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   free_matrix(xi,1,npar,1,npar);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   fclose(ficrespow);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           for (j=1;j<=nlstate+ndeath;j++){
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
+           }
+         for(d=0; d<dh[mi][i]; d++){
- /**** Computes Hessian and covariance matrix ***/
+           newm=savm;
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- {
+           for (kk=1; kk<=cptcovage;kk++) {
-   double  **a,**y,*x,pd;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   double **hess;
+           }
-   int i, j,jk;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   int *indx;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+           oldm=newm;
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+         } /* end mult */
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+         s1=s[mw[mi][i]][i];
-   double gompertz(double p[]);
+         s2=s[mw[mi+1][i]][i];
-   hess=matrix(1,npar,1,npar);
+         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("\nCalculation of the hessian matrix. Wait...\n");
+         ipmx +=1;
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+         sw += weight[i];
-   for (i=1;i<=npar;i++){
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     printf("%d",i);fflush(stdout);
+       } /* end of wave */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     /*  printf(" %f ",p[i]);
+       for(mi=1; mi<= wav[i]-1; mi++){
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   for (i=1;i<=npar;i++) {
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for (j=1;j<=npar;j++)  {
+           }
-       if (j>i) {
+         for(d=0; d<dh[mi][i]; d++){
-         printf(".%d%d",i,j);fflush(stdout);
+           newm=savm;
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         hess[j][i]=hess[i][j];
+           }
-         /*printf(" %lf ",hess[i][j]);*/
-       }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   }
+           savm=oldm;
-   printf("\n");
+           oldm=newm;
-   fprintf(ficlog,"\n");
+         } /* end mult */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+         s1=s[mw[mi][i]][i];
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+         s2=s[mw[mi+1][i]][i];
+         if( s2 > nlstate){
-   a=matrix(1,npar,1,npar);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   y=matrix(1,npar,1,npar);
+         }else{
-   x=vector(1,npar);
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   indx=ivector(1,npar);
+         }
-   for (i=1;i<=npar;i++)
+         ipmx +=1;
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+         sw += weight[i];
-   ludcmp(a,npar,indx,&pd);
+         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]); */
-   for (j=1;j<=npar;j++) {
+       } /* end of wave */
-     for (i=1;i<=npar;i++) x[i]=0;
+     } /* end of individual */
-     x[j]=1;
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-     lubksb(a,npar,indx,x);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for (i=1;i<=npar;i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       matcov[i][j]=x[i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-     }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   printf("\n#Hessian matrix#\n");
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+           }
-   for (i=1;i<=npar;i++) {
+         for(d=0; d<dh[mi][i]; d++){
-     for (j=1;j<=npar;j++) {
+           newm=savm;
-       printf("%.3e ",hess[i][j]);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+           for (kk=1; kk<=cptcovage;kk++) {
-     }
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     printf("\n");
+           }
-     fprintf(ficlog,"\n");
-   }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /* Recompute Inverse */
+           savm=oldm;
-   for (i=1;i<=npar;i++)
+           oldm=newm;
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+         } /* end mult */
-   ludcmp(a,npar,indx,&pd);
+         s1=s[mw[mi][i]][i];
-   /*  printf("\n#Hessian matrix recomputed#\n");
+         s2=s[mw[mi+1][i]][i];
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   for (j=1;j<=npar;j++) {
+         ipmx +=1;
-     for (i=1;i<=npar;i++) x[i]=0;
+         sw += weight[i];
-     x[j]=1;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     lubksb(a,npar,indx,x);
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-     for (i=1;i<=npar;i++){
+       } /* end of wave */
-       y[i][j]=x[i];
+     } /* end of individual */
-       printf("%.3e ",y[i][j]);
+   } /* End of if */
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     }
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     printf("\n");
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     fprintf(ficlog,"\n");
+   return -l;
-   }
+ }
-   */
+ /*************** log-likelihood *************/
-   free_matrix(a,1,npar,1,npar);
+ double funcone( double *x)
-   free_matrix(y,1,npar,1,npar);
+ {
-   free_vector(x,1,npar);
+   /* Same as likeli but slower because of a lot of printf and if */
-   free_ivector(indx,1,npar);
+   int i, ii, j, k, mi, d, kk;
-   free_matrix(hess,1,npar,1,npar);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
+   double lli; /* Individual log likelihood */
- }
+   double llt;
+   int s1, s2;
- /*************** hessian matrix ****************/
+   double bbh, survp;
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   /*extern weight */
- {
+   /* We are differentiating ll according to initial status */
-   int i;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   int l=1, lmax=20;
+   /*for(i=1;i<imx;i++)
-   double k1,k2;
+     printf(" %d\n",s[4][i]);
-   double p2[NPARMAX+1];
+   */
-   double res;
+   cov[1]=1.;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   int k=0,kmax=10;
-   double l1;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   fx=func(x);
+     for(mi=1; mi<= wav[i]-1; mi++){
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-   for(l=0 ; l <=lmax; l++){
+         for (j=1;j<=nlstate+ndeath;j++){
-     l1=pow(10,l);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     delts=delt;
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for(k=1 ; k <kmax; k=k+1){
+         }
-       delt = delta*(l1*k);
+       for(d=0; d<dh[mi][i]; d++){
-       p2[theta]=x[theta] +delt;
+         newm=savm;
-       k1=func(p2)-fx;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       p2[theta]=x[theta]-delt;
+         for (kk=1; kk<=cptcovage;kk++) {
-       k2=func(p2)-fx;
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         }
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- #ifdef DEBUG
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       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);
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-       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);
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
- #endif
+         savm=oldm;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+         oldm=newm;
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+       } /* end mult */
-         k=kmax;
-       }
+       s1=s[mw[mi][i]][i];
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+       s2=s[mw[mi+1][i]][i];
-         k=kmax; l=lmax*10.;
+       bbh=(double)bh[mi][i]/(double)stepm;
-       }
+       /* bias is positive if real duration
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+        * is higher than the multiple of stepm and negative otherwise.
-         delts=delt;
+        */
-       }
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-     }
+         lli=log(out[s1][s2] - savm[s1][s2]);
-   }
+       } else if  (s2==-2) {
-   delti[theta]=delts;
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   return res;
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         lli= log(survp);
- }
+       }else if (mle==1){
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+       } else if(mle==2){
- {
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   int i;
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   int l=1, l1, lmax=20;
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   double k1,k2,k3,k4,res,fx;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   double p2[NPARMAX+1];
+         lli=log(out[s1][s2]); /* Original formula */
-   int k;
+       } else{  /* mle=0 back to 1 */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   fx=func(x);
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   for (k=1; k<=2; k++) {
+       } /* End of if */
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+       ipmx +=1;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       sw += weight[i];
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     k1=func(p2)-fx;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       if(globpr){
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+  %11.6f %11.6f %11.6f ", \
-     k2=func(p2)-fx;
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+           llt +=ll[k]*gipmx/gsw;
-     k3=func(p2)-fx;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+         fprintf(ficresilk," %10.6f\n", -llt);
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       }
-     k4=func(p2)-fx;
+     } /* end of wave */
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+   } /* end of individual */
- #ifdef DEBUG
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     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);
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     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);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
- #endif
+   if(globpr==0){ /* First time we count the contributions and weights */
-   }
+     gipmx=ipmx;
-   return res;
+     gsw=sw;
- }
+   }
+   return -l;
- /************** Inverse of matrix **************/
+ }
- void ludcmp(double **a, int n, int *indx, double *d)
- {
-   int i,imax,j,k;
+ /*************** function likelione ***********/
-   double big,dum,sum,temp;
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-   double *vv;
+ {
+   /* This routine should help understanding what is done with
-   vv=vector(1,n);
+      the selection of individuals/waves and
-   *d=1.0;
+      to check the exact contribution to the likelihood.
-   for (i=1;i<=n;i++) {
+      Plotting could be done.
-     big=0.0;
+    */
-     for (j=1;j<=n;j++)
+   int k;
-       if ((temp=fabs(a[i][j])) > big) big=temp;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     vv[i]=1.0/big;
+     strcpy(fileresilk,"ilk");
-   }
+     strcat(fileresilk,fileres);
-   for (j=1;j<=n;j++) {
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-     for (i=1;i<j;i++) {
+       printf("Problem with resultfile: %s\n", fileresilk);
-       sum=a[i][j];
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+     }
-       a[i][j]=sum;
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-     }
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-     big=0.0;
+     /*  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 (i=j;i<=n;i++) {
+     for(k=1; k<=nlstate; k++)
-       sum=a[i][j];
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-       for (k=1;k<j;k++)
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-         sum -= a[i][k]*a[k][j];
+   }
-       a[i][j]=sum;
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   *fretone=(*funcone)(p);
-         big=dum;
+   if(*globpri !=0){
-         imax=i;
+     fclose(ficresilk);
-       }
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-     }
+     fflush(fichtm);
-     if (j != imax) {
+   }
-       for (k=1;k<=n;k++) {
+   return;
-         dum=a[imax][k];
+ }
-         a[imax][k]=a[j][k];
-         a[j][k]=dum;
-       }
+ /*********** Maximum Likelihood Estimation ***************/
-       *d = -(*d);
-       vv[imax]=vv[j];
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-     }
+ {
-     indx[j]=imax;
+   int i,j, iter=0;
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   double **xi;
-     if (j != n) {
+   double fret;
-       dum=1.0/(a[j][j]);
+   double fretone; /* Only one call to likelihood */
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   /*  char filerespow[FILENAMELENGTH];*/
-     }
-   }
+ #ifdef NLOPT
-   free_vector(vv,1,n);  /* Doesn't work */
+   int creturn;
- ;
+   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 *\/ */
+   double *lb;
- void lubksb(double **a, int n, int *indx, double b[])
+   double minf; /* the minimum objective value, upon return */
- {
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-   int i,ii=0,ip,j;
+   myfunc_data dinst, *d = &dinst;
-   double sum;
+ #endif
-   for (i=1;i<=n;i++) {
-     ip=indx[i];
+   xi=matrix(1,npar,1,npar);
-     sum=b[ip];
+   for (i=1;i<=npar;i++)
-     b[ip]=b[i];
+     for (j=1;j<=npar;j++)
-     if (ii)
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     else if (sum) ii=i;
+   strcpy(filerespow,"pow");
-     b[i]=sum;
+   strcat(filerespow,fileres);
-   }
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   for (i=n;i>=1;i--) {
+     printf("Problem with resultfile: %s\n", filerespow);
-     sum=b[i];
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   }
-     b[i]=sum/a[i][i];
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   }
+   for (i=1;i<=nlstate;i++)
- }
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- void pstamp(FILE *fichier)
+   fprintf(ficrespow,"\n");
- {
+ #ifdef POWELL
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   powell(p,xi,npar,ftol,&iter,&fret,func);
- }
+ #endif
- /************ Frequencies ********************/
+ #ifdef NLOPT
- 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[])
+ #ifdef NEWUOA
- {  /* Some frequencies */
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-   int first;
+ #endif
-   double ***freq; /* Frequencies */
+   lb=vector(0,npar-1);
-   double *pp, **prop;
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   nlopt_set_lower_bounds(opt, lb);
-   char fileresp[FILENAMELENGTH];
+   nlopt_set_initial_step1(opt, 0.1);
-   pp=vector(1,nlstate);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   d->function = func;
-   strcpy(fileresp,"p");
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   strcat(fileresp,fileres);
+   nlopt_set_min_objective(opt, myfunc, d);
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   nlopt_set_xtol_rel(opt, ftol);
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+     printf("nlopt failed! %d\n",creturn);
-     exit(0);
+   }
-   }
+   else {
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   j1=0;
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
+     iter=1; /* not equal */
-   j=cptcoveff;
+   }
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   nlopt_destroy(opt);
+ #endif
-   first=1;
+   free_matrix(xi,1,npar,1,npar);
+   fclose(ficrespow);
-   for(k1=1; k1<=j;k1++){
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-       j1++;
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         scanf("%d", i);*/
+ }
-       for (i=-5; i<=nlstate+ndeath; i++)
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+ /**** Computes Hessian and covariance matrix ***/
-           for(m=iagemin; m <= iagemax+3; m++)
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-             freq[i][jk][m]=0;
+ {
+   double  **a,**y,*x,pd;
-     for (i=1; i<=nlstate; i++)
+   double **hess;
-       for(m=iagemin; m <= iagemax+3; m++)
+   int i, j;
-         prop[i][m]=0;
+   int *indx;
-       dateintsum=0;
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-       k2cpt=0;
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-       for (i=1; i<=imx; i++) {
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-         bool=1;
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-         if  (cptcovn>0) {
+   double gompertz(double p[]);
-           for (z1=1; z1<=cptcoveff; z1++)
+   hess=matrix(1,npar,1,npar);
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-         }
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-         if (bool==1){
+   for (i=1;i<=npar;i++){
-           for(m=firstpass; m<=lastpass; m++){
+     printf("%d",i);fflush(stdout);
-             k2=anint[m][i]+(mint[m][i]/12.);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-               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];
+     /*  printf(" %f ",p[i]);
-               if (m<lastpass) {
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+   }
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-               }
+   for (i=1;i<=npar;i++) {
+     for (j=1;j<=npar;j++)  {
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+       if (j>i) {
-                 dateintsum=dateintsum+k2;
+         printf(".%d%d",i,j);fflush(stdout);
-                 k2cpt++;
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-               }
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-               /*}*/
-           }
+         hess[j][i]=hess[i][j];
-         }
+         /*printf(" %lf ",hess[i][j]);*/
        }
+     }
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+   }
-       pstamp(ficresp);
+   printf("\n");
-       if  (cptcovn>0) {
+   fprintf(ficlog,"\n");
-         fprintf(ficresp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-         fprintf(ficresp, "**********\n#");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       }
-       for(i=1; i<=nlstate;i++)
+   a=matrix(1,npar,1,npar);
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   y=matrix(1,npar,1,npar);
-       fprintf(ficresp, "\n");
+   x=vector(1,npar);
+   indx=ivector(1,npar);
-       for(i=iagemin; i <= iagemax+3; i++){
+   for (i=1;i<=npar;i++)
-         if(i==iagemax+3){
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-           fprintf(ficlog,"Total");
+   ludcmp(a,npar,indx,&pd);
-         }else{
-           if(first==1){
+   for (j=1;j<=npar;j++) {
-             first=0;
+     for (i=1;i<=npar;i++) x[i]=0;
-             printf("See log file for details...\n");
+     x[j]=1;
-           }
+     lubksb(a,npar,indx,x);
-           fprintf(ficlog,"Age %d", i);
+     for (i=1;i<=npar;i++){
-         }
+       matcov[i][j]=x[i];
-         for(jk=1; jk <=nlstate ; jk++){
+     }
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   }
-             pp[jk] += freq[jk][m][i];
-         }
+   printf("\n#Hessian matrix#\n");
-         for(jk=1; jk <=nlstate ; jk++){
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-           for(m=-1, pos=0; m <=0 ; m++)
+   for (i=1;i<=npar;i++) {
-             pos += freq[jk][m][i];
+     for (j=1;j<=npar;j++) {
-           if(pp[jk]>=1.e-10){
+       printf("%.3e ",hess[i][j]);
-             if(first==1){
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     }
-             }
+     printf("\n");
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     fprintf(ficlog,"\n");
-           }else{
+   }
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   /* Recompute Inverse */
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (i=1;i<=npar;i++)
-           }
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-         }
+   ludcmp(a,npar,indx,&pd);
-         for(jk=1; jk <=nlstate ; jk++){
+   /*  printf("\n#Hessian matrix recomputed#\n");
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
+   for (j=1;j<=npar;j++) {
-         }
+     for (i=1;i<=npar;i++) x[i]=0;
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+     x[j]=1;
-           pos += pp[jk];
+     lubksb(a,npar,indx,x);
-           posprop += prop[jk][i];
+     for (i=1;i<=npar;i++){
-         }
+       y[i][j]=x[i];
-         for(jk=1; jk <=nlstate ; jk++){
+       printf("%.3e ",y[i][j]);
-           if(pos>=1.e-5){
+       fprintf(ficlog,"%.3e ",y[i][j]);
-             if(first==1)
+     }
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     printf("\n");
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     fprintf(ficlog,"\n");
-           }else{
+   }
-             if(first==1)
+   */
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   free_matrix(a,1,npar,1,npar);
-           }
+   free_matrix(y,1,npar,1,npar);
-           if( i <= iagemax){
+   free_vector(x,1,npar);
-             if(pos>=1.e-5){
+   free_ivector(indx,1,npar);
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   free_matrix(hess,1,npar,1,npar);
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-             }
+ }
-             else
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+ /*************** hessian matrix ****************/
-           }
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-         }
+ {
+   int i;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+   int l=1, lmax=20;
-           for(m=-1; m <=nlstate+ndeath; m++)
+   double k1,k2;
-             if(freq[jk][m][i] !=0 ) {
+   double p2[MAXPARM+1]; /* identical to x */
-             if(first==1)
+   double res;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+   double fx;
-             }
+   int k=0,kmax=10;
-         if(i <= iagemax)
+   double l1;
-           fprintf(ficresp,"\n");
-         if(first==1)
+   fx=func(x);
-           printf("Others in log...\n");
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-         fprintf(ficlog,"\n");
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-       }
+     l1=pow(10,l);
-     }
+     delts=delt;
-   }
+     for(k=1 ; k <kmax; k=k+1){
-   dateintmean=dateintsum/k2cpt;
+       delt = delta*(l1*k);
+       p2[theta]=x[theta] +delt;
-   fclose(ficresp);
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+       p2[theta]=x[theta]-delt;
-   free_vector(pp,1,nlstate);
+       k2=func(p2)-fx;
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   /* End of Freq */
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
- }
+ #ifdef DEBUGHESS
- /************ Prevalence ********************/
+       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);
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
- {
+ #endif
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-      We still use firstpass and lastpass as another selection.
+         k=kmax;
-   */
+       }
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+         k=kmax; l=lmax*10;
-   double ***freq; /* Frequencies */
+       }
-   double *pp, **prop;
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   double pos,posprop;
+         delts=delt;
-   double  y2; /* in fractional years */
+       }
-   int iagemin, iagemax;
+     }
+   }
-   iagemin= (int) agemin;
+   delti[theta]=delts;
-   iagemax= (int) agemax;
+   return res;
-   /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+ }
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   j1=0;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ {
-   j=cptcoveff;
+   int i;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   int l=1, lmax=20;
+   double k1,k2,k3,k4,res,fx;
-   for(k1=1; k1<=j;k1++){
+   double p2[MAXPARM+1];
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   int k;
-       j1++;
+   fx=func(x);
-       for (i=1; i<=nlstate; i++)
+   for (k=1; k<=2; k++) {
-         for(m=iagemin; m <= iagemax+3; m++)
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-           prop[i][m]=0.0;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-       for (i=1; i<=imx; i++) { /* Each individual */
+     k1=func(p2)-fx;
-         bool=1;
-         if  (cptcovn>0) {
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-           for (z1=1; z1<=cptcoveff; z1++)
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     k2=func(p2)-fx;
-               bool=0;
-         }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-         if (bool==1) {
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+     k3=func(p2)-fx;
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     k4=func(p2)-fx;
-               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);
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+ #ifdef DEBUG
-                 /*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]]);*/
+     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);
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-                 prop[s[m][i]][iagemax+3] += weight[i];
+ #endif
-               }
+   }
-             }
+   return res;
-           } /* end selection of waves */
+ }
-         }
-       }
+ /************** Inverse of matrix **************/
-       for(i=iagemin; i <= iagemax+3; i++){
+ void ludcmp(double **a, int n, int *indx, double *d)
+ {
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+   int i,imax,j,k;
-           posprop += prop[jk][i];
+   double big,dum,sum,temp;
-         }
+   double *vv;
-         for(jk=1; jk <=nlstate ; jk++){
+   vv=vector(1,n);
-           if( i <=  iagemax){
+   *d=1.0;
-             if(posprop>=1.e-5){
+   for (i=1;i<=n;i++) {
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+     big=0.0;
-             }
+     for (j=1;j<=n;j++)
-           }
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-         }/* end jk */
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-       }/* end i */
+     vv[i]=1.0/big;
-     } /* end i1 */
+   }
-   } /* end k1 */
+   for (j=1;j<=n;j++) {
+     for (i=1;i<j;i++) {
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+       sum=a[i][j];
-   /*free_vector(pp,1,nlstate);*/
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+       a[i][j]=sum;
- }  /* End of prevalence */
+     }
+     big=0.0;
- /************* Waves Concatenation ***************/
+     for (i=j;i<=n;i++) {
+       sum=a[i][j];
- void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+       for (k=1;k<j;k++)
- {
+         sum -= a[i][k]*a[k][j];
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       a[i][j]=sum;
-      Death is a valid wave (if date is known).
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+         big=dum;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+         imax=i;
-      and mw[mi+1][i]. dh depends on stepm.
+       }
-      */
+     }
+     if (j != imax) {
-   int i, mi, m;
+       for (k=1;k<=n;k++) {
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+         dum=a[imax][k];
-      double sum=0., jmean=0.;*/
+         a[imax][k]=a[j][k];
-   int first;
+         a[j][k]=dum;
-   int j, k=0,jk, ju, jl;
+       }
-   double sum=0.;
+       *d = -(*d);
-   first=0;
+       vv[imax]=vv[j];
-   jmin=1e+5;
+     }
-   jmax=-1;
+     indx[j]=imax;
-   jmean=0.;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   for(i=1; i<=imx; i++){
+     if (j != n) {
-     mi=0;
+       dum=1.0/(a[j][j]);
-     m=firstpass;
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-     while(s[m][i] <= nlstate){
+     }
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+   }
-         mw[++mi][i]=m;
+   free_vector(vv,1,n);  /* Doesn't work */
-       if(m >=lastpass)
+ ;
-         break;
+ }
-       else
-         m++;
+ void lubksb(double **a, int n, int *indx, double b[])
-     }/* end while */
+ {
-     if (s[m][i] > nlstate){
+   int i,ii=0,ip,j;
-       mi++;     /* Death is another wave */
+   double sum;
-       /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
+   for (i=1;i<=n;i++) {
-       mw[mi][i]=m;
+     ip=indx[i];
-     }
+     sum=b[ip];
+     b[ip]=b[i];
-     wav[i]=mi;
+     if (ii)
-     if(mi==0){
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-       nbwarn++;
+     else if (sum) ii=i;
-       if(first==0){
+     b[i]=sum;
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+   }
-         first=1;
+   for (i=n;i>=1;i--) {
-       }
+     sum=b[i];
-       if(first==1){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+     b[i]=sum/a[i][i];
-       }
+   }
-     } /* end mi==0 */
+ }
-   } /* End individuals */
+ void pstamp(FILE *fichier)
-   for(i=1; i<=imx; i++){
+ {
-     for(mi=1; mi<wav[i];mi++){
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-       if (stepm <=0)
+ }
-         dh[mi][i]=1;
-       else{
+ /************ Frequencies ********************/
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-           if (agedc[i] < 2*AGESUP) {
+ {  /* Some frequencies */
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-             if(j==0) j=1;  /* Survives at least one month after exam */
+   int i, m, jk, j1, bool, z1,j;
-             else if(j<0){
+   int first;
-               nberr++;
+   double ***freq; /* Frequencies */
-               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]);
+   double *pp, **prop;
-               j=1; /* Temporary Dangerous patch */
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-               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);
+   char fileresp[FILENAMELENGTH];
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   pp=vector(1,nlstate);
-             }
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-             k=k+1;
+   strcpy(fileresp,"p");
-             if (j >= jmax){
+   strcat(fileresp,fileres);
-               jmax=j;
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-               ijmax=i;
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-             }
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-             if (j <= jmin){
+     exit(0);
-               jmin=j;
+   }
-               ijmin=i;
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-             }
+   j1=0;
-             sum=sum+j;
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   j=cptcoveff;
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           }
-         }
+   first=1;
-         else{
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
- /*        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]); */
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+   /*    j1++;
-           k=k+1;
+ */
-           if (j >= jmax) {
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-             jmax=j;
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-             ijmax=i;
+         scanf("%d", i);*/
-           }
+       for (i=-5; i<=nlstate+ndeath; i++)
-           else if (j <= jmin){
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-             jmin=j;
+           for(m=iagemin; m <= iagemax+3; m++)
-             ijmin=i;
+             freq[i][jk][m]=0;
-           }
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+       for (i=1; i<=nlstate; i++)
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+         for(m=iagemin; m <= iagemax+3; m++)
-           if(j<0){
+           prop[i][m]=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]);
+       dateintsum=0;
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+       k2cpt=0;
-           }
+       for (i=1; i<=imx; i++) {
-           sum=sum+j;
+         bool=1;
-         }
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-         jk= j/stepm;
+           for (z1=1; z1<=cptcoveff; z1++)
-         jl= j -jk*stepm;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-         ju= j -(jk+1)*stepm;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+               bool=0;
-           if(jl==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",
-             dh[mi][i]=jk;
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-             bh[mi][i]=0;
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-           }else{ /* We want a negative bias in order to only have interpolation ie
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-                   * at the price of an extra matrix product in likelihood */
+             }
-             dh[mi][i]=jk+1;
+         }
-             bh[mi][i]=ju;
-           }
+         if (bool==1){
-         }else{
+           for(m=firstpass; m<=lastpass; m++){
-           if(jl <= -ju){
+             k2=anint[m][i]+(mint[m][i]/12.);
-             dh[mi][i]=jk;
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-             bh[mi][i]=jl;       /* bias is positive if real duration
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-                                  * is higher than the multiple of stepm and negative otherwise.
+               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) {
-           else{
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-             dh[mi][i]=jk+1;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-             bh[mi][i]=ju;
+               }
-           }
-           if(dh[mi][i]==0){
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-             dh[mi][i]=1; /* At least one step */
+                 dateintsum=dateintsum+k2;
-             bh[mi][i]=ju; /* At least one step */
+                 k2cpt++;
-             /*  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);*/
+               }
-           }
+               /*}*/
-         } /* end if mle */
+           }
-       }
+         }
-     } /* end wave */
+       } /* end i */
-   }
-   jmean=sum/k;
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   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);
+       pstamp(ficresp);
-   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  (cptcovn>0) {
-  }
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- /*********** Tricode ****************************/
+         fprintf(ficresp, "**********\n#");
- void tricode(int *Tvar, int **nbcode, int imx)
+         fprintf(ficlog, "\n#********** Variable ");
- {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficlog, "**********\n#");
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+       }
-   int cptcode=0;
+       for(i=1; i<=nlstate;i++)
-   cptcoveff=0;
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, "\n");
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+       for(i=iagemin; i <= iagemax+3; i++){
+         if(i==iagemax+3){
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+           fprintf(ficlog,"Total");
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+         }else{
-                                modality*/
+           if(first==1){
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+             first=0;
-       Ndum[ij]++; /*store the modality */
+             printf("See log file for details...\n");
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+           }
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+           fprintf(ficlog,"Age %d", i);
-                                        Tvar[j]. If V=sex and male is 0 and
+         }
-                                        female is 1, then  cptcode=1.*/
+         for(jk=1; jk <=nlstate ; jk++){
-     }
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
-     for (i=0; i<=cptcode; i++) {
+         }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+         for(jk=1; jk <=nlstate ; jk++){
-     }
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[jk][m][i];
-     ij=1;
+           if(pp[jk]>=1.e-10){
-     for (i=1; i<=ncodemax[j]; i++) {
+             if(first==1){
-       for (k=0; k<= maxncov; k++) {
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-         if (Ndum[k] != 0) {
+             }
-           nbcode[Tvar[j]][ij]=k;
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           /* 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; */
+           }else{
+             if(first==1)
-           ij++;
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         }
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         if (ij > ncodemax[j]) break;
+           }
-       }
+         }
-     }
-   }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+             pp[jk] += freq[jk][m][i];
+         }
-  for (i=1; i<=ncovmodel-2; i++) {
+         for(jk=1,pos=0,posprop=0; 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.*/
+           pos += pp[jk];
-    ij=Tvar[i];
+           posprop += prop[jk][i];
-    Ndum[ij]++;
+         }
-  }
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5){
-  ij=1;
+             if(first==1)
-  for (i=1; i<= maxncov; i++) {
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-      Tvaraff[ij]=i; /*For printing */
+           }else{
-      ij++;
+             if(first==1)
-    }
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-  }
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
-  cptcoveff=ij-1; /*Number of simple covariates*/
+           if( i <= iagemax){
- }
+             if(pos>=1.e-5){
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
- /*********** Health Expectancies ****************/
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
- 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[] )
+             }
+             else
- {
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-   /* Health expectancies, no variances */
+           }
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+         }
-   double age, agelim, hf;
-   double ***p3mat;
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-   double eip;
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) {
-   pstamp(ficreseij);
+             if(first==1)
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   fprintf(ficreseij,"# Age");
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   for(i=1; i<=nlstate;i++){
+             }
-     for(j=1; j<=nlstate;j++){
+         if(i <= iagemax)
-       fprintf(ficreseij," e%1d%1d ",i,j);
+           fprintf(ficresp,"\n");
-     }
+         if(first==1)
-     fprintf(ficreseij," e%1d. ",i);
+           printf("Others in log...\n");
-   }
+         fprintf(ficlog,"\n");
-   fprintf(ficreseij,"\n");
+       }
+       /*}*/
+   }
-   if(estepm < stepm){
+   dateintmean=dateintsum/k2cpt;
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
+   fclose(ficresp);
-   else  hstepm=estepm;
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   free_vector(pp,1,nlstate);
-    * This is mainly to measure the difference between two models: for example
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   /* End of Freq */
-    * 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
+ /************ Prevalence ********************/
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ 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)
-    * to compare the new estimate of Life expectancy with the same linear
+ {
-    * hypothesis. A more precise result, taking into account a more precise
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-    * curvature will be obtained if estepm is as small as stepm. */
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
+   int i, m, jk, j1, bool, z1,j;
-      nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+   double **prop;
-      and note for a fixed period like estepm months */
+   double posprop;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   double  y2; /* in fractional years */
-      survival function given by stepm (the optimization length). Unfortunately it
+   int iagemin, iagemax;
-      means that if the survival funtion is printed only each two years of age and if
+   int first; /** to stop verbosity which is redirected to log file */
-      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.
+   iagemin= (int) agemin;
-   */
+   iagemax= (int) agemax;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   agelim=AGESUP;
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   /* If stepm=6 months */
+   j1=0;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   /*j=cptcoveff;*/
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
- /* nhstepm age range expressed in number of stepm */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   first=1;
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-   /* if (stepm >= YEARM) hstepm=1;*/
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       j1++;*/
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (i=1; i<=nlstate; i++)
-   for (age=bage; age<=fage; age ++){
+         for(m=iagemin; m <= iagemax+3; m++)
+           prop[i][m]=0.0;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       for (i=1; i<=imx; i++) { /* Each individual */
+         bool=1;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+         if  (cptcovn>0) {
+           for (z1=1; z1<=cptcoveff; z1++)
-     printf("%d|",(int)age);fflush(stdout);
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+               bool=0;
+         }
+         if (bool==1) {
-     /* Computing expectancies */
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-     for(i=1; i<=nlstate;i++)
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-       for(j=1; j<=nlstate;j++)
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+               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);
-           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+               if (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]]);*/
-         }
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-     fprintf(ficreseij,"%3.0f",age );
+               }
-     for(i=1; i<=nlstate;i++){
+             }
-       eip=0;
+           } /* end selection of waves */
-       for(j=1; j<=nlstate;j++){
+         }
-         eip +=eij[i][j][(int)age];
+       }
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       for(i=iagemin; i <= iagemax+3; i++){
-       }
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-       fprintf(ficreseij,"%9.4f", eip );
+           posprop += prop[jk][i];
-     }
+         }
-     fprintf(ficreseij,"\n");
+         for(jk=1; jk <=nlstate ; jk++){
-   }
+           if( i <=  iagemax){
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             if(posprop>=1.e-5){
-   printf("\n");
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-   fprintf(ficlog,"\n");
+             } else{
+               if(first==1){
- }
+                 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]);
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+               }
+             }
- {
+           }
-   /* Covariances of health expectancies eij and of total life expectancies according
+         }/* end jk */
-    to initial status i, ei. .
+       }/* end i */
-   */
+     /*} *//* end i1 */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   } /* end j1 */
-   double age, agelim, hf;
-   double ***p3matp, ***p3matm, ***varhe;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   double **dnewm,**doldm;
+   /*free_vector(pp,1,nlstate);*/
-   double *xp, *xm;
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   double **gp, **gm;
+ }  /* End of prevalence */
-   double ***gradg, ***trgradg;
-   int theta;
+ /************* Waves Concatenation ***************/
-   double eip, vip;
+ 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)
+ {
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   xp=vector(1,npar);
+      Death is a valid wave (if date is known).
-   xm=vector(1,npar);
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+      and mw[mi+1][i]. dh depends on stepm.
+      */
-   pstamp(ficresstdeij);
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   int i, mi, m;
-   fprintf(ficresstdeij,"# Age");
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   for(i=1; i<=nlstate;i++){
+      double sum=0., jmean=0.;*/
-     for(j=1; j<=nlstate;j++)
+   int first;
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   int j, k=0,jk, ju, jl;
-     fprintf(ficresstdeij," e%1d. ",i);
+   double sum=0.;
-   }
+   first=0;
-   fprintf(ficresstdeij,"\n");
+   jmin=100000;
+   jmax=-1;
-   pstamp(ficrescveij);
+   jmean=0.;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   for(i=1; i<=imx; i++){
-   fprintf(ficrescveij,"# Age");
+     mi=0;
-   for(i=1; i<=nlstate;i++)
+     m=firstpass;
-     for(j=1; j<=nlstate;j++){
+     while(s[m][i] <= nlstate){
-       cptj= (j-1)*nlstate+i;
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-       for(i2=1; i2<=nlstate;i2++)
+         mw[++mi][i]=m;
-         for(j2=1; j2<=nlstate;j2++){
+       if(m >=lastpass)
-           cptj2= (j2-1)*nlstate+i2;
+         break;
-           if(cptj2 <= cptj)
+       else
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         m++;
-         }
+     }/* end while */
-     }
+     if (s[m][i] > nlstate){
-   fprintf(ficrescveij,"\n");
+       mi++;     /* Death is another wave */
+       /* if(mi==0)  never been interviewed correctly before death */
-   if(estepm < stepm){
+          /* Only death is a correct wave */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       mw[mi][i]=m;
-   }
+     }
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     wav[i]=mi;
-    * This is mainly to measure the difference between two models: for example
+     if(mi==0){
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+       nbwarn++;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       if(first==0){
-    * progression in between and thus overestimating or underestimating according
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-    * to the curvature of the survival function. If, for the same date, we
+         first=1;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+       }
-    * to compare the new estimate of Life expectancy with the same linear
+       if(first==1){
-    * hypothesis. A more precise result, taking into account a more precise
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-    * curvature will be obtained if estepm is as small as stepm. */
+       }
+     } /* end mi==0 */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   } /* End individuals */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
+   for(i=1; i<=imx; i++){
-      nstepm is the number of stepm from age to agelin.
+     for(mi=1; mi<wav[i];mi++){
-      Look at hpijx to understand the reason of that which relies in memory size
+       if (stepm <=0)
-      and note for a fixed period like estepm months */
+         dh[mi][i]=1;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       else{
-      survival function given by stepm (the optimization length). Unfortunately it
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-      means that if the survival funtion is printed only each two years of age and if
+           if (agedc[i] < 2*AGESUP) {
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-      results. So we changed our mind and took the option of the best precision.
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   */
+             else if(j<0){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+               nberr++;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   /* If stepm=6 months */
+               j=1; /* Temporary Dangerous patch */
-   /* nhstepm age range expressed in number of stepm */
+               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);
-   agelim=AGESUP;
+               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]);
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+               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);
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+             }
-   /* if (stepm >= YEARM) hstepm=1;*/
+             k=k+1;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+             if (j >= jmax){
+               jmax=j;
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               ijmax=i;
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             }
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+             if (j <= jmin){
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+               jmin=j;
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+               ijmin=i;
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+             }
+             sum=sum+j;
-   for (age=bage; age<=fage; age ++){
+             /*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);*/
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           }
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         }
+         else{
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-     /* Computing  Variances of health expectancies */
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+           k=k+1;
-        decrease memory allocation */
+           if (j >= jmax) {
-     for(theta=1; theta <=npar; theta++){
+             jmax=j;
-       for(i=1; i<=npar; i++){
+             ijmax=i;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           }
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+           else if (j <= jmin){
-       }
+             jmin=j;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+             ijmin=i;
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+           }
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-       for(j=1; j<= nlstate; j++){
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-         for(i=1; i<=nlstate; i++){
+           if(j<0){
-           for(h=0; h<=nhstepm-1; h++){
+             nberr++;
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             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]);
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
            }
-         }
+           sum=sum+j;
-       }
+         }
+         jk= j/stepm;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+         jl= j -jk*stepm;
-         for(h=0; h<=nhstepm-1; h++){
+         ju= j -(jk+1)*stepm;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-         }
+           if(jl==0){
-     }/* End theta */
+             dh[mi][i]=jk;
+             bh[mi][i]=0;
+           }else{ /* We want a negative bias in order to only have interpolation ie
-     for(h=0; h<=nhstepm-1; h++)
+                   * to avoid the price of an extra matrix product in likelihood */
-       for(j=1; j<=nlstate*nlstate;j++)
+             dh[mi][i]=jk+1;
-         for(theta=1; theta <=npar; theta++)
+             bh[mi][i]=ju;
-           trgradg[h][j][theta]=gradg[h][theta][j];
+           }
+         }else{
+           if(jl <= -ju){
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+             dh[mi][i]=jk;
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         varhe[ij][ji][(int)age] =0.;
+                                  * is higher than the multiple of stepm and negative otherwise.
+                                  */
-      printf("%d|",(int)age);fflush(stdout);
+           }
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           else{
-      for(h=0;h<=nhstepm-1;h++){
+             dh[mi][i]=jk+1;
-       for(k=0;k<=nhstepm-1;k++){
+             bh[mi][i]=ju;
-         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]);
+           if(dh[mi][i]==0){
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+             dh[mi][i]=1; /* At least one step */
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+             bh[mi][i]=ju; /* At least one step */
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+             /*  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);*/
-       }
+           }
-     }
+         } /* end if mle */
+       }
-     /* Computing expectancies */
+     } /* end wave */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   }
-     for(i=1; i<=nlstate;i++)
+   jmean=sum/k;
-       for(j=1; j<=nlstate;j++)
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   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);
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+  }
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+ /*********** Tricode ****************************/
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-         }
+ {
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-     fprintf(ficresstdeij,"%3.0f",age );
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-     for(i=1; i<=nlstate;i++){
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
-       eip=0.;
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-       vip=0.;
+   /* nbcode[Tvar[j]][1]=
-       for(j=1; j<=nlstate;j++){
+   */
-         eip += eij[i][j][(int)age];
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+   int modmaxcovj=0; /* Modality max of covariates j */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+   int cptcode=0; /* Modality max of covariates j */
-       }
+   int modmincovj=0; /* Modality min of covariates j */
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-     }
-     fprintf(ficresstdeij,"\n");
+   cptcoveff=0;
-     fprintf(ficrescveij,"%3.0f",age );
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-     for(i=1; i<=nlstate;i++)
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-       for(j=1; j<=nlstate;j++){
-         cptj= (j-1)*nlstate+i;
+   /* Loop on covariates without age and products */
-         for(i2=1; i2<=nlstate;i2++)
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-           for(j2=1; j2<=nlstate;j2++){
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-             cptj2= (j2-1)*nlstate+i2;
+                                modality of this covariate Vj*/
-             if(cptj2 <= cptj)
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+                                     * If product of Vn*Vm, still boolean *:
-           }
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-       }
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-     fprintf(ficrescveij,"\n");
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+                                       modality of the nth covariate of individual i. */
-   }
+       if (ij > modmaxcovj)
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+         modmaxcovj=ij;
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+       else if (ij < modmincovj)
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+         modmincovj=ij;
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+       if ((ij < -1) && (ij > NCOVMAX)){
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         exit(1);
-   printf("\n");
+       }else
-   fprintf(ficlog,"\n");
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   free_vector(xm,1,npar);
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-   free_vector(xp,1,npar);
+       /* getting the maximum value of the modality of the covariate
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+          female is 1, then modmaxcovj=1.*/
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+     }
- }
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+     cptcode=modmaxcovj;
- /************ Variance ******************/
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+    /*for (i=0; i<=cptcode; i++) {*/
- {
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-   /* Variance of health expectancies */
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-   /* double **newm;*/
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-   double **dnewm,**doldm;
+       }
-   double **dnewmp,**doldmp;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   int i, j, nhstepm, hstepm, h, nstepm ;
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   int k, cptcode;
+     } /* Ndum[-1] number of undefined modalities */
-   double *xp;
-   double **gp, **gm;  /* for var eij */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-   double ***gradg, ***trgradg; /*for var eij */
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-   double **gradgp, **trgradgp; /* for var p point j */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-   double *gpp, *gmp; /* for var p point j */
+        modmincovj=3; modmaxcovj = 7;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
-   double ***p3mat;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-   double age,agelim, hf;
+        variables V1_1 and V1_2.
-   double ***mobaverage;
+        nbcode[Tvar[j]][ij]=k;
-   int theta;
+        nbcode[Tvar[j]][1]=0;
-   char digit[4];
+        nbcode[Tvar[j]][2]=1;
-   char digitp[25];
+        nbcode[Tvar[j]][3]=2;
+     */
-   char fileresprobmorprev[FILENAMELENGTH];
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   if(popbased==1){
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-     if(mobilav!=0)
+         /*recode from 0 */
-       strcpy(digitp,"-populbased-mobilav-");
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-     else strcpy(digitp,"-populbased-nomobil-");
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   }
+                                      k is a modality. If we have model=V1+V1*sex
-   else
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-     strcpy(digitp,"-stablbased-");
+           ij++;
+         }
-   if (mobilav!=0) {
+         if (ij > ncodemax[j]) break;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       }  /* end of loop on */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     } /* end of loop on modality */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   }
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-   strcpy(fileresprobmorprev,"prmorprev");
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-   sprintf(digit,"%-d",ij);
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    Ndum[ij]++;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+  }
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+  ij=1;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-   }
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+      Tvaraff[ij]=i; /*For printing (unclear) */
+      ij++;
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    }else
-   pstamp(ficresprobmorprev);
+        Tvaraff[ij]=0;
-   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);
+  ij--;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+  cptcoveff=ij; /*Number of total covariates*/
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
+ }
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
-   fprintf(ficresprobmorprev,"\n");
+ /*********** Health Expectancies ****************/
-   fprintf(ficgp,"\n# Routine varevsij");
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ {
- /*   } */
+   /* Health expectancies, no variances */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   int i, j, nhstepm, hstepm, h, nstepm;
-   pstamp(ficresvij);
+   int nhstepma, nstepma; /* Decreasing with age */
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   double age, agelim, hf;
-   if(popbased==1)
+   double ***p3mat;
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+   double eip;
-   else
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   pstamp(ficreseij);
-   fprintf(ficresvij,"# Age");
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficreseij,"# Age");
-     for(j=1; j<=nlstate;j++)
+   for(i=1; i<=nlstate;i++){
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+     for(j=1; j<=nlstate;j++){
-   fprintf(ficresvij,"\n");
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
-   xp=vector(1,npar);
+     fprintf(ficreseij," e%1d. ",i);
-   dnewm=matrix(1,nlstate,1,npar);
+   }
-   doldm=matrix(1,nlstate,1,nlstate);
+   fprintf(ficreseij,"\n");
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if(estepm < stepm){
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   }
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   else  hstepm=estepm;
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-   if(estepm < stepm){
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   }
+    * progression in between and thus overestimating or underestimating according
-   else  hstepm=estepm;
+    * to the curvature of the survival function. If, for the same date, we
-   /* For example we decided to compute the life expectancy with the smallest unit */
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+    * to compare the new estimate of Life expectancy with the same linear
-      nhstepm is the number of hstepm from age to agelim
+    * hypothesis. A more precise result, taking into account a more precise
-      nstepm is the number of stepm from age to agelin.
+    * curvature will be obtained if estepm is as small as stepm. */
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like k years */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      survival function given by stepm (the optimization length). Unfortunately it
+      nhstepm is the number of hstepm from age to agelim
-      means that if the survival funtion is printed every two years of age and if
+      nstepm is the number of stepm from age to agelin.
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      Look at hpijx to understand the reason of that which relies in memory size
-      results. So we changed our mind and took the option of the best precision.
+      and note for a fixed period like estepm months */
-   */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+      survival function given by stepm (the optimization length). Unfortunately it
-   agelim = AGESUP;
+      means that if the survival funtion is printed only each two years of age and if
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+      results. So we changed our mind and took the option of the best precision.
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
+   agelim=AGESUP;
-     gm=matrix(0,nhstepm,1,nlstate);
+   /* 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 */
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+ /* nhstepm age range expressed in number of stepm */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       }
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   /* if (stepm >= YEARM) hstepm=1;*/
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       if (popbased==1) {
-         if(mobilav ==0){
+   for (age=bage; age<=fage; age ++){
-           for(i=1; i<=nlstate;i++)
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-             prlim[i][i]=probs[(int)age][i][ij];
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         }else{ /* mobilav */
+     /* if (stepm >= YEARM) hstepm=1;*/
-           for(i=1; i<=nlstate;i++)
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+     /* If stepm=6 months */
-       }
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         }
-       }
+     printf("%d|",(int)age);fflush(stdout);
-       /* This for computing probability of death (h=1 means
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+     /* Computing expectancies */
-       */
+     for(i=1; i<=nlstate;i++)
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for(j=1; j<=nlstate;j++)
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       }
-       /* end probability of death */
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+         }
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     fprintf(ficreseij,"%3.0f",age );
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     for(i=1; i<=nlstate;i++){
+       eip=0;
-       if (popbased==1) {
+       for(j=1; j<=nlstate;j++){
-         if(mobilav ==0){
+         eip +=eij[i][j][(int)age];
-           for(i=1; i<=nlstate;i++)
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-             prlim[i][i]=probs[(int)age][i][ij];
+       }
-         }else{ /* mobilav */
+       fprintf(ficreseij,"%9.4f", eip );
-           for(i=1; i<=nlstate;i++)
+     }
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     fprintf(ficreseij,"\n");
-         }
-       }
+   }
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(j=1; j<= nlstate; j++){
+   printf("\n");
-         for(h=0; h<=nhstepm; h++){
+   fprintf(ficlog,"\n");
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+ }
-         }
-       }
+ 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[] )
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+ {
-          as a weighted average of prlim.
+   /* Covariances of health expectancies eij and of total life expectancies according
-       */
+    to initial status i, ei. .
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   */
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   int nhstepma, nstepma; /* Decreasing with age */
-       }
+   double age, agelim, hf;
-       /* end probability of death */
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
-       for(j=1; j<= nlstate; j++) /* vareij */
+   double *xp, *xm;
-         for(h=0; h<=nhstepm; h++){
+   double **gp, **gm;
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   double ***gradg, ***trgradg;
-         }
+   int theta;
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   double eip, vip;
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-       }
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   xp=vector(1,npar);
-     } /* End theta */
+   xm=vector(1,npar);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-     for(h=0; h<=nhstepm; h++) /* veij */
+   pstamp(ficresstdeij);
-       for(j=1; j<=nlstate;j++)
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-         for(theta=1; theta <=npar; theta++)
+   fprintf(ficresstdeij,"# Age");
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++)
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       for(theta=1; theta <=npar; theta++)
+     fprintf(ficresstdeij," e%1d. ",i);
-         trgradgp[j][theta]=gradgp[theta][j];
+   }
+   fprintf(ficresstdeij,"\n");
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   pstamp(ficrescveij);
-     for(i=1;i<=nlstate;i++)
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-       for(j=1;j<=nlstate;j++)
+   fprintf(ficrescveij,"# Age");
-         vareij[i][j][(int)age] =0.;
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
-     for(h=0;h<=nhstepm;h++){
+       cptj= (j-1)*nlstate+i;
-       for(k=0;k<=nhstepm;k++){
+       for(i2=1; i2<=nlstate;i2++)
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         for(j2=1; j2<=nlstate;j2++){
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+           cptj2= (j2-1)*nlstate+i2;
-         for(i=1;i<=nlstate;i++)
+           if(cptj2 <= cptj)
-           for(j=1;j<=nlstate;j++)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+         }
-       }
+     }
-     }
+   fprintf(ficrescveij,"\n");
-     /* pptj */
+   if(estepm < stepm){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+   }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+   else  hstepm=estepm;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-         varppt[j][i]=doldmp[j][i];
+    * This is mainly to measure the difference between two models: for example
-     /* end ppptj */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     /*  x centered again */
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+    * progression in between and thus overestimating or underestimating according
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-     if (popbased==1) {
+    * to compare the new estimate of Life expectancy with the same linear
-       if(mobilav ==0){
+    * hypothesis. A more precise result, taking into account a more precise
-         for(i=1; i<=nlstate;i++)
+    * curvature will be obtained if estepm is as small as stepm. */
-           prlim[i][i]=probs[(int)age][i][ij];
-       }else{ /* mobilav */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         for(i=1; i<=nlstate;i++)
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+      nhstepm is the number of hstepm from age to agelim
-       }
+      nstepm is the number of stepm from age to agelin.
-     }
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
-     /* This for computing probability of death (h=1 means
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+      survival function given by stepm (the optimization length). Unfortunately it
-        as a weighted average of prlim.
+      means that if the survival funtion is printed only each two years of age and if
-     */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+      results. So we changed our mind and took the option of the best precision.
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   */
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     }
-     /* end probability of death */
+   /* If stepm=6 months */
+   /* nhstepm age range expressed in number of stepm */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+   agelim=AGESUP;
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(i=1; i<=nlstate;i++){
+   /* if (stepm >= YEARM) hstepm=1;*/
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       }
-     }
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficresprobmorprev,"\n");
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     fprintf(ficresvij,"%.0f ",age );
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     for(i=1; i<=nlstate;i++)
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-       for(j=1; j<=nlstate;j++){
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-       }
+   for (age=bage; age<=fage; age ++){
-     fprintf(ficresvij,"\n");
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     free_matrix(gp,0,nhstepm,1,nlstate);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     free_matrix(gm,0,nhstepm,1,nlstate);
+     /* if (stepm >= YEARM) hstepm=1;*/
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /* If stepm=6 months */
-   } /* End age */
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     /* Computing  Variances of health expectancies */
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+        decrease memory allocation */
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+     for(theta=1; theta <=npar; theta++){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       for(i=1; i<=npar; i++){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+       }
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   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(j=1; j<= nlstate; j++){
- */
+         for(i=1; i<=nlstate; i++){
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+           for(h=0; h<=nhstepm-1; h++){
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+             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.;
-   free_vector(xp,1,npar);
+           }
-   free_matrix(doldm,1,nlstate,1,nlstate);
+         }
-   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);
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         for(h=0; h<=nhstepm-1; h++){
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   fclose(ficresprobmorprev);
+         }
-   fflush(ficgp);
+     }/* End theta */
-   fflush(fichtm);
- }  /* end varevsij */
+     for(h=0; h<=nhstepm-1; h++)
- /************ Variance of prevlim ******************/
+       for(j=1; j<=nlstate*nlstate;j++)
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+         for(theta=1; theta <=npar; theta++)
- {
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   double **dnewm,**doldm;
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   int i, j, nhstepm, hstepm;
+         varhe[ij][ji][(int)age] =0.;
-   int k, cptcode;
-   double *xp;
+      printf("%d|",(int)age);fflush(stdout);
-   double *gp, *gm;
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   double **gradg, **trgradg;
+      for(h=0;h<=nhstepm-1;h++){
-   double age,agelim;
+       for(k=0;k<=nhstepm-1;k++){
-   int theta;
+         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]);
-   pstamp(ficresvpl);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   fprintf(ficresvpl,"# Age");
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   for(i=1; i<=nlstate;i++)
+       }
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     }
-   fprintf(ficresvpl,"\n");
+     /* Computing expectancies */
-   xp=vector(1,npar);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   dnewm=matrix(1,nlstate,1,npar);
+     for(i=1; i<=nlstate;i++)
-   doldm=matrix(1,nlstate,1,nlstate);
+       for(j=1; j<=nlstate;j++)
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   hstepm=1*YEARM; /* Every year of age */
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         }
-     if (stepm >= YEARM) hstepm=1;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     fprintf(ficresstdeij,"%3.0f",age );
-     gradg=matrix(1,npar,1,nlstate);
+     for(i=1; i<=nlstate;i++){
-     gp=vector(1,nlstate);
+       eip=0.;
-     gm=vector(1,nlstate);
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
-     for(theta=1; theta <=npar; theta++){
+         eip += eij[i][j][(int)age];
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-       }
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       for(i=1;i<=nlstate;i++)
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-         gp[i] = prlim[i][i];
+     }
+     fprintf(ficresstdeij,"\n");
-       for(i=1; i<=npar; i++) /* Computes gradient */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     fprintf(ficrescveij,"%3.0f",age );
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     for(i=1; i<=nlstate;i++)
-       for(i=1;i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-         gm[i] = prlim[i][i];
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-       for(i=1;i<=nlstate;i++)
+           for(j2=1; j2<=nlstate;j2++){
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+             cptj2= (j2-1)*nlstate+i2;
-     } /* End theta */
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-     trgradg =matrix(1,nlstate,1,npar);
+           }
+       }
-     for(j=1; j<=nlstate;j++)
+     fprintf(ficrescveij,"\n");
-       for(theta=1; theta <=npar; theta++)
-         trgradg[j][theta]=gradg[theta][j];
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     for(i=1;i<=nlstate;i++)
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-       varpl[i][(int)age] =0.;
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(i=1;i<=nlstate;i++)
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   printf("\n");
+   fprintf(ficlog,"\n");
-     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+   free_vector(xm,1,npar);
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   free_vector(xp,1,npar);
-     fprintf(ficresvpl,"\n");
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-     free_vector(gp,1,nlstate);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-     free_vector(gm,1,nlstate);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-     free_matrix(gradg,1,npar,1,nlstate);
+ }
-     free_matrix(trgradg,1,nlstate,1,npar);
-   } /* End age */
+ /************ Variance ******************/
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
-   free_vector(xp,1,npar);
+ {
-   free_matrix(doldm,1,nlstate,1,npar);
+   /* Variance of health expectancies */
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /* double **newm;*/
- }
+   double **dnewm,**doldm;
+   double **dnewmp,**doldmp;
- /************ Variance of one-step probabilities  ******************/
+   int i, j, nhstepm, hstepm, h, nstepm ;
- 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[])
+   int k;
- {
+   double *xp;
-   int i, j=0,  i1, k1, l1, t, tj;
+   double **gp, **gm;  /* for var eij */
-   int k2, l2, j1,  z1;
+   double ***gradg, ***trgradg; /*for var eij */
-   int k=0,l, cptcode;
+   double **gradgp, **trgradgp; /* for var p point j */
-   int first=1, first1;
+   double *gpp, *gmp; /* for var p point j */
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   double **dnewm,**doldm;
+   double ***p3mat;
-   double *xp;
+   double age,agelim, hf;
-   double *gp, *gm;
+   double ***mobaverage;
-   double **gradg, **trgradg;
+   int theta;
-   double **mu;
+   char digit[4];
-   double age,agelim, cov[NCOVMAX];
+   char digitp[25];
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+   char fileresprobmorprev[FILENAMELENGTH];
-   char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+   if(popbased==1){
-   char fileresprobcor[FILENAMELENGTH];
+     if(mobilav!=0)
+       strcpy(digitp,"-populbased-mobilav-");
-   double ***varpij;
+     else strcpy(digitp,"-populbased-nomobil-");
+   }
-   strcpy(fileresprob,"prob");
+   else
-   strcat(fileresprob,fileres);
+     strcpy(digitp,"-stablbased-");
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprob);
+   if (mobilav!=0) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   }
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   strcpy(fileresprobcov,"probcov");
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   strcat(fileresprobcov,fileres);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     }
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   }
+   strcpy(fileresprobmorprev,"prmorprev");
-   strcpy(fileresprobcor,"probcor");
+   sprintf(digit,"%-d",ij);
-   strcat(fileresprobcor,fileres);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   strcat(fileresprobmorprev,fileres);
-   }
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   }
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   pstamp(ficresprob);
+   pstamp(ficresprobmorprev);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprob,"# Age");
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   pstamp(ficresprobcov);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   fprintf(ficresprobcov,"# Age");
+     for(i=1; i<=nlstate;i++)
-   pstamp(ficresprobcor);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   }
-   fprintf(ficresprobcor,"# Age");
+   fprintf(ficresprobmorprev,"\n");
+   fprintf(ficgp,"\n# Routine varevsij");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   for(i=1; i<=nlstate;i++)
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-     for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+ /*   } */
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   pstamp(ficresvij);
-     }
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-  /* fprintf(ficresprob,"\n");
+   if(popbased==1)
-   fprintf(ficresprobcov,"\n");
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   fprintf(ficresprobcor,"\n");
+   else
-  */
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-  xp=vector(1,npar);
+   fprintf(ficresvij,"# Age");
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   for(i=1; i<=nlstate;i++)
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+     for(j=1; j<=nlstate;j++)
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   fprintf(ficresvij,"\n");
-   first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+   xp=vector(1,npar);
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   dnewm=matrix(1,nlstate,1,npar);
-   fprintf(fichtm,"\n");
+   doldm=matrix(1,nlstate,1,nlstate);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   file %s<br>\n",optionfilehtmcov);
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   gpp=vector(nlstate+1,nlstate+ndeath);
- and drawn. It helps understanding how is the covariance between two incidences.\
+   gmp=vector(nlstate+1,nlstate+ndeath);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   if(estepm < stepm){
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+     printf ("Problem %d lower than %d\n",estepm, stepm);
- standard deviations wide on each axis. <br>\
+   }
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+   else  hstepm=estepm;
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   /* For example we decided to compute the life expectancy with the smallest unit */
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
-   cov[1]=1;
+      nstepm is the number of stepm from age to agelin.
-   tj=cptcoveff;
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   j1=0;
+      survival function given by stepm (the optimization length). Unfortunately it
-   for(t=1; t<=tj;t++){
+      means that if the survival funtion is printed every two years of age and if
-     for(i1=1; i1<=ncodemax[t];i1++){
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-       j1++;
+      results. So we changed our mind and took the option of the best precision.
-       if  (cptcovn>0) {
+   */
-         fprintf(ficresprob, "\n#********** Variable ");
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   agelim = AGESUP;
-         fprintf(ficresprob, "**********\n#\n");
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         fprintf(ficresprobcov, "\n#********** Variable ");
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         fprintf(ficresprobcov, "**********\n#\n");
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         fprintf(ficgp, "\n#********** Variable ");
+     gp=matrix(0,nhstepm,1,nlstate);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     gm=matrix(0,nhstepm,1,nlstate);
-         fprintf(ficgp, "**********\n#\n");
+     for(theta=1; theta <=npar; theta++){
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+       }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresprobcor, "**********\n#");
+       if (popbased==1) {
-       }
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-       for (age=bage; age<=fage; age ++){
+             prlim[i][i]=probs[(int)age][i][ij];
-         cov[2]=age;
+         }else{ /* mobilav */
-         for (k=1; k<=cptcovn;k++) {
+           for(i=1; i<=nlstate;i++)
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+             prlim[i][i]=mobaverage[(int)age][i][ij];
          }
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       }
-         for (k=1; k<=cptcovprod;k++)
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       for(j=1; j<= nlstate; j++){
+         for(h=0; h<=nhstepm; h++){
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         }
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+       }
+       /* This for computing probability of death (h=1 means
-         for(theta=1; theta <=npar; theta++){
+          computed over hstepm matrices product = hstepm*stepm months)
-           for(i=1; i<=npar; i++)
+          as a weighted average of prlim.
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-           k=0;
+       }
-           for(i=1; i<= (nlstate); i++){
+       /* end probability of death */
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-               gp[k]=pmmij[i][j];
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-             }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-           }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           for(i=1; i<=npar; i++)
+       if (popbased==1) {
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+             prlim[i][i]=probs[(int)age][i][ij];
-           k=0;
+         }else{ /* mobilav */
-           for(i=1; i<=(nlstate); i++){
+           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=(nlstate+ndeath);j++){
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-               k=k+1;
+         }
-               gm[k]=pmmij[i][j];
+       }
-             }
-           }
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+         for(h=0; h<=nhstepm; h++){
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
+       }
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+       /* This for computing probability of death (h=1 means
-           for(theta=1; theta <=npar; theta++)
+          computed over hstepm matrices product = hstepm*stepm months)
-             trgradg[j][theta]=gradg[theta][j];
+          as a weighted average of prlim.
+       */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+       }
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       /* end probability of death */
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       for(j=1; j<= nlstate; j++) /* vareij */
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         for(h=0; h<=nhstepm; h++){
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         k=0;
+         }
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-             k=k+1;
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-             mu[k][(int) age]=pmmij[i][j];
+       }
-           }
-         }
+     } /* End theta */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-             varpij[i][j][(int)age] = doldm[i][j];
+     for(h=0; h<=nhstepm; h++) /* veij */
-         /*printf("\n%d ",(int)age);
+       for(j=1; j<=nlstate;j++)
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         for(theta=1; theta <=npar; theta++)
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           trgradg[h][j][theta]=gradg[h][theta][j];
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
-         fprintf(ficresprob,"\n%d ",(int)age);
+         trgradgp[j][theta]=gradgp[theta][j];
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+     for(i=1;i<=nlstate;i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+       for(j=1;j<=nlstate;j++)
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         vareij[i][j][(int)age] =0.;
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+     for(h=0;h<=nhstepm;h++){
-         }
+       for(k=0;k<=nhstepm;k++){
-         i=0;
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-         for (k=1; k<=(nlstate);k++){
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-           for (l=1; l<=(nlstate+ndeath);l++){
+         for(i=1;i<=nlstate;i++)
-             i=i++;
+           for(j=1;j<=nlstate;j++)
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+       }
-             for (j=1; j<=i;j++){
+     }
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+     /* pptj */
-             }
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-           }
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-         }/* end of loop for state */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-       } /* end of loop for age */
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         varppt[j][i]=doldmp[j][i];
-       /* Confidence intervalle of pij  */
+     /* end ppptj */
-       /*
+     /*  x centered again */
-         fprintf(ficgp,"\nset noparametric;unset label");
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-         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);
+     if (popbased==1) {
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+       if(mobilav ==0){
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         for(i=1; i<=nlstate;i++)
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+           prlim[i][i]=probs[(int)age][i][ij];
-       */
+       }else{ /* mobilav */
+         for(i=1; i<=nlstate;i++)
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-       first1=1;
+       }
-       for (k2=1; k2<=(nlstate);k2++){
+     }
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
+     /* This for computing probability of death (h=1 means
-           j=(k2-1)*(nlstate+ndeath)+l2;
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-           for (k1=1; k1<=(nlstate);k1++){
+        as a weighted average of prlim.
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+     */
-               if(l1==k1) continue;
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-               i=(k1-1)*(nlstate+ndeath)+l1;
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-               if(i<=j) continue;
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-               for (age=bage; age<=fage; age ++){
+     }
-                 if ((int)age %5==0){
+     /* end probability of death */
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+       for(i=1; i<=nlstate;i++){
-                   c12=cv12/sqrt(v1*v2);
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-                   /* Computing eigen value of matrix of covariance */
+       }
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     }
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     fprintf(ficresprobmorprev,"\n");
-                   /* Eigen vectors */
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     fprintf(ficresvij,"%.0f ",age );
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+     for(i=1; i<=nlstate;i++)
-                   v21=(lc1-v1)/cv12*v11;
+       for(j=1; j<=nlstate;j++){
-                   v12=-v21;
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-                   v22=v11;
+       }
-                   tnalp=v21/v11;
+     fprintf(ficresvij,"\n");
-                   if(first1==1){
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                     first1=0;
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                     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);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                   }
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-                   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);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                   /*printf(fignu*/
+   } /* End age */
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                   if(first==1){
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                     first=0;
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-                     fprintf(ficgp,"\nset parametric;unset label");
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
-                     fprintf(ficgp,"\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",\
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-                   }else{
+   free_vector(xp,1,npar);
-                     first=0;
+   free_matrix(doldm,1,nlstate,1,nlstate);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   free_matrix(dnewm,1,nlstate,1,npar);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-                     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",\
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   fclose(ficresprobmorprev);
-                   }/* if first */
+   fflush(ficgp);
-                 } /* age mod 5 */
+   fflush(fichtm);
-               } /* end loop age */
+ }  /* end varevsij */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-               first=1;
+ /************ Variance of prevlim ******************/
-             } /*l12 */
+ 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[])
-           } /* k12 */
+ {
-         } /*l1 */
+   /* Variance of prevalence limit */
-       }/* k1 */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-     } /* loop covariates */
-   }
+   double **dnewm,**doldm;
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   int i, j, nhstepm, hstepm;
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   double *xp;
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   double *gp, *gm;
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   double **gradg, **trgradg;
-   free_vector(xp,1,npar);
+   double age,agelim;
-   fclose(ficresprob);
+   int theta;
-   fclose(ficresprobcov);
-   fclose(ficresprobcor);
+   pstamp(ficresvpl);
-   fflush(ficgp);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fflush(fichtmcov);
+   fprintf(ficresvpl,"# Age");
- }
+   for(i=1; i<=nlstate;i++)
+       fprintf(ficresvpl," %1d-%1d",i,i);
+   fprintf(ficresvpl,"\n");
- /******************* Printing html file ***********/
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   xp=vector(1,npar);
-                   int lastpass, int stepm, int weightopt, char model[],\
+   dnewm=matrix(1,nlstate,1,npar);
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   doldm=matrix(1,nlstate,1,nlstate);
-                   int popforecast, int estepm ,\
-                   double jprev1, double mprev1,double anprev1, \
+   hstepm=1*YEARM; /* Every year of age */
-                   double jprev2, double mprev2,double anprev2){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   int jj1, k1, i1, cpt;
+   agelim = AGESUP;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+     if (stepm >= YEARM) hstepm=1;
- </ul>");
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+     gradg=matrix(1,npar,1,nlstate);
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+     gp=vector(1,nlstate);
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+     gm=vector(1,nlstate);
-    fprintf(fichtm,"\
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+     for(theta=1; theta <=npar; theta++){
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-    fprintf(fichtm,"\
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+       }
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-    fprintf(fichtm,"\
+       for(i=1;i<=nlstate;i++)
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+         gp[i] = prlim[i][i];
-    <a href=\"%s\">%s</a> <br>\n",
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+       for(i=1; i<=npar; i++) /* Computes gradient */
-    fprintf(fichtm,"\
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-  - Population projections by age and states: \
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+       for(i=1;i<=nlstate;i++)
+         gm[i] = prlim[i][i];
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+       for(i=1;i<=nlstate;i++)
-  m=cptcoveff;
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+     } /* End theta */
-  jj1=0;
+     trgradg =matrix(1,nlstate,1,npar);
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     for(j=1; j<=nlstate;j++)
-      jj1++;
+       for(theta=1; theta <=npar; theta++)
-      if (cptcovn > 0) {
+         trgradg[j][theta]=gradg[theta][j];
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+     for(i=1;i<=nlstate;i++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       varpl[i][(int)age] =0.;
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-      }
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-      /* 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%d1.png\">%s%d1.png</a><br> \
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-      /* Quasi-incidences */
+     fprintf(ficresvpl,"%.0f ",age );
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+     for(i=1; i<=nlstate;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> \
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+     fprintf(ficresvpl,"\n");
-        /* Period (stable) prevalence in each health state */
+     free_vector(gp,1,nlstate);
-        for(cpt=1; cpt<nlstate;cpt++){
+     free_vector(gm,1,nlstate);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+     free_matrix(gradg,1,npar,1,nlstate);
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+     free_matrix(trgradg,1,nlstate,1,npar);
-        }
+   } /* End age */
-      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 : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+   free_vector(xp,1,npar);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+   free_matrix(doldm,1,nlstate,1,npar);
-      }
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-    } /* end i1 */
-  }/* End k1 */
+ }
-  fprintf(fichtm,"</ul>");
+ /************ Variance of one-step probabilities  ******************/
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-  fprintf(fichtm,"\
+ {
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   int i, j=0,  k1, l1, tj;
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   int k2, l2, j1,  z1;
+   int k=0, l;
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   int first=1, first1, first2;
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-  fprintf(fichtm,"\
+   double **dnewm,**doldm;
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   double *xp;
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   double *gp, *gm;
+   double **gradg, **trgradg;
-  fprintf(fichtm,"\
+   double **mu;
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   double age, cov[NCOVMAX+1];
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-  fprintf(fichtm,"\
+   int theta;
-  - 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 fileresprob[FILENAMELENGTH];
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   char fileresprobcov[FILENAMELENGTH];
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   char fileresprobcor[FILENAMELENGTH];
-  fprintf(fichtm,"\
+   double ***varpij;
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   strcpy(fileresprob,"prob");
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   strcat(fileresprob,fileres);
-  fprintf(fichtm,"\
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-  - 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",
+     printf("Problem with resultfile: %s\n", fileresprob);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-  fprintf(fichtm,"\
+   }
-  - 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",
+   strcpy(fileresprobcov,"probcov");
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   strcat(fileresprobcov,fileres);
-  fprintf(fichtm,"\
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   strcpy(fileresprobcor,"probcor");
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   strcat(fileresprobcor,fileres);
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
- /*      <br>",fileres,fileres,fileres,fileres); */
+     printf("Problem with resultfile: %s\n", fileresprobcor);
- /*  else  */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+   }
-  fflush(fichtm);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   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);
-  m=cptcoveff;
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-  jj1=0;
+   pstamp(ficresprob);
-  for(k1=1; k1<=m;k1++){
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   fprintf(ficresprob,"# Age");
-      jj1++;
+   pstamp(ficresprobcov);
-      if (cptcovn > 0) {
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   fprintf(ficresprobcov,"# Age");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   pstamp(ficresprobcor);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fprintf(ficresprobcor,"# Age");
-      }
-      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   for(i=1; i<=nlstate;i++)
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+     for(j=1; j<=(nlstate+ndeath);j++){
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-      }
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
- health expectancies in states (1) and (2): %s%d.png<br>\
+     }
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+  /* fprintf(ficresprob,"\n");
-    } /* end i1 */
+   fprintf(ficresprobcov,"\n");
-  }/* End k1 */
+   fprintf(ficresprobcor,"\n");
-  fprintf(fichtm,"</ul>");
+  */
-  fflush(fichtm);
+   xp=vector(1,npar);
- }
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- /******************* Gnuplot file **************/
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
-   char dirfileres[132],optfileres[132];
+   fprintf(ficgp,"\n# Routine varprob");
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   int ng;
+   fprintf(fichtm,"\n");
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
- /*     printf("Problem with file %s",optionfilegnuplot); */
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
- /*   } */
+   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   /*#ifdef windows */
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-     /*#endif */
+   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. \
-   m=pow(2,cptcoveff);
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-   strcpy(dirfileres,optionfilefiname);
+ standard deviations wide on each axis. <br>\
-   strcpy(optfileres,"vpl");
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-  /* 1eme*/
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-    for (k1=1; k1<= m ; k1 ++) {
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   cov[1]=1;
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+   /* tj=cptcoveff; */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+   tj = (int) pow(2,cptcoveff);
- set ylabel \"Probability\" \n\
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
- set ter png small\n\
+   j1=0;
- set size 0.65,0.65\n\
+   for(j1=1; j1<=tj;j1++){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+     /*j1++;*/
-      for (i=1; i<= nlstate ; i ++) {
+       if  (cptcovn>0) {
-        if (i==cpt) 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");
-      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(ficresprobcov, "\n#********** Variable ");
-      for (i=1; i<= nlstate ; i ++) {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficresprobcov, "**********\n#\n");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+         fprintf(ficgp, "\n#********** Variable ");
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      for (i=1; i<= nlstate ; i ++) {
+         fprintf(ficgp, "**********\n#\n");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    }
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-   }
-   /*2 eme*/
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (k1=1; k1<= m ; k1 ++) {
+         fprintf(ficresprobcor, "**********\n#");
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+       }
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-     for (i=1; i<= nlstate+1 ; i ++) {
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       k=2*i;
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-       for (j=1; j<= nlstate+1 ; j ++) {
+       for (age=bage; age<=fage; age ++){
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         cov[2]=age;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for (k=1; k<=cptcovn;k++) {
-       }
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+                                                          * 1  1 1 1 1
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+                                                          * 2  2 1 1 1
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                          * 3  1 2 1 1
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                          */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         }
-       }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       fprintf(ficgp,"\" t\"\" w l 0,");
+         for (k=1; k<=cptcovprod;k++)
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for(theta=1; theta <=npar; theta++){
-       }
+           for(i=1; i<=npar; i++)
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       else fprintf(ficgp,"\" t\"\" w l 0,");
-     }
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   }
+           k=0;
-   /*3eme*/
+           for(i=1; i<= (nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
-   for (k1=1; k1<= m ; k1 ++) {
+               k=k+1;
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+               gp[k]=pmmij[i][j];
-       /*       k=2+nlstate*(2*cpt-2); */
+             }
-       k=2+(nlstate+1)*(cpt-1);
+           }
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+           for(i=1; i<=npar; i++)
- set size 0.65,0.65\n\
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           k=0;
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           for(i=1; i<=(nlstate); i++){
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+             for(j=1; j<=(nlstate+ndeath);j++){
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+               k=k+1;
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+               gm[k]=pmmij[i][j];
+             }
-       */
+           }
-       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(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-         /*      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);*/
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         }
-       }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-     }
+           for(theta=1; theta <=npar; theta++)
-   }
+             trgradg[j][theta]=gradg[theta][j];
-   /* CV preval stable (period) */
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-   for (k1=1; k1<= m ; k1 ++) {
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
-       k=3;
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         k=0;
- set ter png small\nset size 0.65,0.65\n\
+         for(i=1; i<=(nlstate); i++){
- unset log y\n\
+           for(j=1; j<=(nlstate+ndeath);j++){
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+             k=k+1;
+             mu[k][(int) age]=pmmij[i][j];
-       for (i=1; i< nlstate ; i ++)
+           }
-         fprintf(ficgp,"+$%d",k+i+1);
+         }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-       l=3+(nlstate+ndeath)*cpt;
+             varpij[i][j][(int)age] = doldm[i][j];
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-       for (i=1; i< nlstate ; i ++) {
+         /*printf("\n%d ",(int)age);
-         l=3+(nlstate+ndeath)*cpt;
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-         fprintf(ficgp,"+$%d",l+i+1);
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-       }
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+           }*/
-     }
-   }
+         fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-   /* proba elementaires */
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-   for(i=1,jk=1; i <=nlstate; i++){
-     for(k=1; k <=(nlstate+ndeath); k++){
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-       if (k != i) {
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for(j=1; j <=ncovmodel; j++){
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           jk++;
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficgp,"\n");
+         }
-         }
+         i=0;
-       }
+         for (k=1; k<=(nlstate);k++){
-     }
+           for (l=1; l<=(nlstate+ndeath);l++){
-    }
+             i++;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-      for(jk=1; jk <=m; jk++) {
+             for (j=1; j<=i;j++){
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-        if (ng==2)
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-        else
+             }
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+           }
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         }/* end of loop for state */
-        i=1;
+       } /* end of loop for age */
-        for(k2=1; k2<=nlstate; k2++) {
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-          k3=i;
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-          for(k=1; k<=(nlstate+ndeath); k++) {
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-            if (k != k2){
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-              if(ng==2)
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+       /* Confidence intervalle of pij  */
-              else
+       /*
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+         fprintf(ficgp,"\nunset parametric;unset label");
-              ij=1;
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-              for(j=3; j <=ncovmodel; j++) {
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-                  ij++;
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-                }
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-                else
+       */
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-              }
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-              fprintf(ficgp,")/(1");
+       first1=1;first2=2;
+       for (k2=1; k2<=(nlstate);k2++){
-              for(k1=1; k1 <=nlstate; k1++){
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+           if(l2==k2) continue;
-                ij=1;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-                for(j=3; j <=ncovmodel; j++){
+           for (k1=1; k1<=(nlstate);k1++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+               if(l1==k1) continue;
-                    ij++;
+               i=(k1-1)*(nlstate+ndeath)+l1;
-                  }
+               if(i<=j) continue;
-                  else
+               for (age=bage; age<=fage; age ++){
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                 if ((int)age %5==0){
-                }
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                fprintf(ficgp,")");
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-              }
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-              i=i+ncovmodel;
+                   c12=cv12/sqrt(v1*v2);
-            }
+                   /* Computing eigen value of matrix of covariance */
-          } /* end k */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-        } /* end k2 */
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-      } /* end jk */
+                   if ((lc2 <0) || (lc1 <0) ){
-    } /* end ng */
+                     if(first2==1){
-    fflush(ficgp);
+                       first1=0;
- }  /* end gnuplot */
+                     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);
+                     }
+                     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);
- /*************** Moving average **************/
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                     /* lc2=fabs(lc2); */
+                   }
-   int i, cpt, cptcod;
-   int modcovmax =1;
+                   /* Eigen vectors */
-   int mobilavrange, mob;
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-   double age;
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                   v12=-v21;
-                            a covariate has 2 modalities */
+                   v22=v11;
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                   tnalp=v21/v11;
+                   if(first1==1){
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+                     first1=0;
-     if(mobilav==1) mobilavrange=5; /* default */
+                     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);
-     else mobilavrange=mobilav;
+                   }
-     for (age=bage; age<=fage; age++)
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-       for (i=1; i<=nlstate;i++)
+                   /*printf(fignu*/
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-     /* We keep the original values on the extreme ages bage, fage and for
+                   if(first==1){
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                     first=0;
-        we use a 5 terms etc. until the borders are no more concerned.
+                     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);
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-         for (i=1; i<=nlstate;i++){
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                     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);
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-           }
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-         }
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-       }/* end age */
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-     }/* end mob */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-   }else return -1;
+                   }else{
-   return 0;
+                     first=0;
- }/* End movingaverage */
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- /************** Forecasting ******************/
+                     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",\
- 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,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-   /* proj1, year, month, day of starting projection
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-      agemin, agemax range of age
+                   }/* if first */
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+                 } /* age mod 5 */
-      anproj2 year of en of projection (same day and month as proj1).
+               } /* end loop age */
-   */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+               first=1;
-   int *popage;
+             } /*l12 */
-   double agec; /* generic age */
+           } /* k12 */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+         } /*l1 */
-   double *popeffectif,*popcount;
+       }/* k1 */
-   double ***p3mat;
+       /* } /* loop covariates */
-   double ***mobaverage;
+   }
-   char fileresf[FILENAMELENGTH];
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   agelim=AGESUP;
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   free_vector(xp,1,npar);
-   strcpy(fileresf,"f");
+   fclose(ficresprob);
-   strcat(fileresf,fileres);
+   fclose(ficresprobcov);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+   fclose(ficresprobcor);
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+   fflush(ficgp);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   fflush(fichtmcov);
-   }
+ }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+ /******************* Printing html file ***********/
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
-   if (mobilav!=0) {
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                   int popforecast, int estepm ,\
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+                   double jprev1, double mprev1,double anprev1, \
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                   double jprev2, double mprev2,double anprev2){
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   int jj1, k1, i1, cpt;
-     }
-   }
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ </ul>");
-   if (stepm<=12) stepsize=1;
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-   if(estepm < stepm){
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   }
+    fprintf(fichtm,"\
-   else  hstepm=estepm;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   hstepm=hstepm/stepm;
+    fprintf(fichtm,"\
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-                                fractional in yp1 */
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-   anprojmean=yp;
+    fprintf(fichtm,"\
-   yp2=modf((yp1*12),&yp);
+  - (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): \
-   mprojmean=yp;
+    <a href=\"%s\">%s</a> <br>\n",
-   yp1=modf((yp2*30.5),&yp);
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-   jprojmean=yp;
+    fprintf(fichtm,"\
-   if(jprojmean==0) jprojmean=1;
+  - Population projections by age and states: \
-   if(mprojmean==0) jprojmean=1;
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   i1=cptcoveff;
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   if (cptcovn < 1){i1=1;}
+  m=pow(2,cptcoveff);
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
- /*            if (h==(int)(YEARM*yearp)){ */
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+      jj1++;
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      if (cptcovn > 0) {
-       k=k+1;
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-       fprintf(ficresf,"\n#******");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-       for(j=1;j<=cptcoveff;j++) {
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-         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(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-       }
+      }
-       fprintf(ficresf,"******\n");
+      /* Pij */
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-       for(j=1; j<=nlstate+ndeath;j++){
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-         for(i=1; i<=nlstate;i++)
+      /* Quasi-incidences */
-           fprintf(ficresf," p%d%d",i,j);
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-         fprintf(ficresf," p.%d",j);
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-       }
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+        /* Period (stable) prevalence in each health state */
-         fprintf(ficresf,"\n");
+        for(cpt=1; cpt<=nlstate;cpt++){
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+          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> \
+ <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+        }
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-           nhstepm = nhstepm/hstepm;
+         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> \
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-           oldm=oldms;savm=savms;
+      }
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+    } /* end i1 */
+  }/* End k1 */
-           for (h=0; h<=nhstepm; h++){
+  fprintf(fichtm,"</ul>");
-             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
-               for(j=1;j<=cptcoveff;j++)
+  fprintf(fichtm,"\
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               ppij=0.;
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-               for(i=1; i<=nlstate;i++) {
+  fprintf(fichtm,"\
-                 if (mobilav==1)
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-                 else {
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+  fprintf(fichtm,"\
-                 }
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                 if (h*hstepm/YEARM*stepm== yearp) {
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+  fprintf(fichtm,"\
-                 }
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
-               } /* end i */
+    <a href=\"%s\">%s</a> <br>\n</li>",
-               if (h*hstepm/YEARM*stepm==yearp) {
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-                 fprintf(ficresf," %.3f", ppij);
+  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): \
-             }/* end j */
+    <a href=\"%s\">%s</a> <br>\n</li>",
-           } /* end h */
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  fprintf(fichtm,"\
-         } /* end agec */
+  - 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",
-       } /* end yearp */
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-     } /* end cptcod */
+  fprintf(fichtm,"\
-   } /* end  cptcov */
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  fprintf(fichtm,"\
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-   fclose(ficresf);
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
- }
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
- /************** Forecasting *****not tested NB*************/
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- 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){
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+ /*      <br>",fileres,fileres,fileres,fileres); */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+ /*  else  */
-   int *popage;
+ /*    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 calagedatem, agelim, kk1, kk2;
+  fflush(fichtm);
-   double *popeffectif,*popcount;
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
+  m=pow(2,cptcoveff);
-   char filerespop[FILENAMELENGTH];
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  jj1=0;
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  for(k1=1; k1<=m;k1++){
-   agelim=AGESUP;
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+      jj1++;
+      if (cptcovn > 0) {
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   strcpy(filerespop,"pop");
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   strcat(filerespop,fileres);
+      }
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ 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);
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+      }
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ true period expectancies (those weighted with period prevalences are also\
+  drawn in addition to the population based expectancies computed using\
-   if (mobilav!=0) {
+  observed and cahotic prevalences: %s%d.png<br>\
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+    } /* end i1 */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+  }/* End k1 */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+  fprintf(fichtm,"</ul>");
-     }
+  fflush(fichtm);
-   }
+ }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /******************* Gnuplot file **************/
-   if (stepm<=12) stepsize=1;
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   agelim=AGESUP;
+   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;
-   hstepm=1;
+   int ng=0;
-   hstepm=hstepm/stepm;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   if (popforecast==1) {
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*   } */
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+   /*#ifdef windows */
-     }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     popage=ivector(0,AGESUP);
+     /*#endif */
-     popeffectif=vector(0,AGESUP);
+   m=pow(2,cptcoveff);
-     popcount=vector(0,AGESUP);
+   strcpy(dirfileres,optionfilefiname);
-     i=1;
+   strcpy(optfileres,"vpl");
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+  /* 1eme*/
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-     imx=i;
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-   }
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ set ylabel \"Probability\" \n\
-       k=k+1;
+ set ter png small size 320, 240\n\
-       fprintf(ficrespop,"\n#******");
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      for (i=1; i<= nlstate ; i ++) {
-       }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       fprintf(ficrespop,"******\n");
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-       fprintf(ficrespop,"# Age");
+      }
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+      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 (popforecast==1)  fprintf(ficrespop," [Population]");
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       for (cpt=0; cpt<=0;cpt++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+      }
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+      for (i=1; i<= nlstate ; i ++) {
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-           nhstepm = nhstepm/hstepm;
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-           oldm=oldms;savm=savms;
+    }
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   }
+   /*2 eme*/
-           for (h=0; h<=nhstepm; h++){
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   for (k1=1; k1<= m ; k1 ++) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+     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);
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
+     for (i=1; i<= nlstate+1 ; i ++) {
-               for(i=1; i<=nlstate;i++) {
+       k=2*i;
-                 if (mobilav==1)
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+       for (j=1; j<= nlstate+1 ; j ++) {
-                 else {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-                 }
+       }
-               }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-               if (h==(int)(calagedatem+12*cpt)){
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                   /*fprintf(ficrespop," %.3f", kk1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-               }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-             }
+       }
-             for(i=1; i<=nlstate;i++){
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-               kk1=0.;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                 for(j=1; j<=nlstate;j++){
+       for (j=1; j<= nlstate+1 ; j ++) {
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                 }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+       }
-             }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+     }
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+   }
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /*3eme*/
-         }
-       }
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-   /******/
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-           nhstepm = nhstepm/hstepm;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-           oldm=oldms;savm=savms;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       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(j=1; j<=nlstate+ndeath;j++) {
+         /*      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);*/
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
+       }
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-               }
+     }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   }
-             }
-           }
+   /* CV preval stable (period) */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   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);
-   }
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ set ter png small size 320, 240\n\
+ unset log y\n\
-   if (popforecast==1) {
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     free_ivector(popage,0,AGESUP);
+       for (i=1; i<= nlstate ; i ++){
-     free_vector(popeffectif,0,AGESUP);
+         if(i==1)
-     free_vector(popcount,0,AGESUP);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-   }
+         else
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           fprintf(ficgp,", '' ");
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         l=(nlstate+ndeath)*(i-1)+1;
-   fclose(ficrespop);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
- } /* End of popforecast */
+         for (j=1; j<= (nlstate-1) ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j);
- int fileappend(FILE *fichier, char *optionfich)
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
- {
+       } /* nlstate */
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+       fprintf(ficgp,"\n");
-     printf("Problem with file: %s\n", optionfich);
+     } /* end cpt state*/
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   } /* end covariate */
-     return (0);
-   }
+   /* proba elementaires */
-   fflush(fichier);
+   for(i=1,jk=1; i <=nlstate; i++){
-   return (1);
+     for(k=1; k <=(nlstate+ndeath); k++){
- }
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
- /**************** function prwizard **********************/
+           jk++;
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+           fprintf(ficgp,"\n");
- {
+         }
+       }
-   /* Wizard to print covariance matrix template */
+     }
+    }
-   char ca[32], cb[32], cc[32];
+   /*goto avoid;*/
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   int numlinepar;
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+        if (ng==2)
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-   for(i=1; i <=nlstate; i++){
+        else
-     jj=0;
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     for(j=1; j <=nlstate+ndeath; j++){
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-       if(j==i) continue;
+        i=1;
-       jj++;
+        for(k2=1; k2<=nlstate; k2++) {
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+          k3=i;
-       printf("%1d%1d",i,j);
+          for(k=1; k<=(nlstate+ndeath); k++) {
-       fprintf(ficparo,"%1d%1d",i,j);
+            if (k != k2){
-       for(k=1; k<=ncovmodel;k++){
+              if(ng==2)
-         /*        printf(" %lf",param[i][j][k]); */
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+              else
-         printf(" 0.");
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-         fprintf(ficparo," 0.");
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-       }
+              for(j=3; j <=ncovmodel; j++) {
-       printf("\n");
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-       fprintf(ficparo,"\n");
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-     }
+                /*        ij++; */
-   }
+                /* } */
-   printf("# Scales (for hessian or gradient estimation)\n");
+                /* else */
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+              }
-   for(i=1; i <=nlstate; i++){
+              fprintf(ficgp,")/(1");
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+              for(k1=1; k1 <=nlstate; k1++){
-       if(j==i) continue;
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-       jj++;
+                ij=1;
-       fprintf(ficparo,"%1d%1d",i,j);
+                for(j=3; j <=ncovmodel; j++){
-       printf("%1d%1d",i,j);
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-       fflush(stdout);
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-       for(k=1; k<=ncovmodel;k++){
+                  /*   ij++; */
-         /*      printf(" %le",delti3[i][j][k]); */
+                  /* } */
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+                  /* else */
-         printf(" 0.");
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-         fprintf(ficparo," 0.");
+                }
-       }
+                fprintf(ficgp,")");
-       numlinepar++;
+              }
-       printf("\n");
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-       fprintf(ficparo,"\n");
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-     }
+              i=i+ncovmodel;
-   }
+            }
-   printf("# Covariance matrix\n");
+          } /* end k */
- /* # 121 Var(a12)\n\ */
+        } /* end k2 */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+      } /* end jk */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+    } /* end ng */
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+  /* avoid: */
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+    fflush(ficgp);
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ }  /* end gnuplot */
- /* # 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" */
-   fflush(stdout);
+ /*************** Moving average **************/
-   fprintf(ficparo,"# Covariance matrix\n");
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-   /* # 121 Var(a12)\n\ */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   int i, cpt, cptcod;
-   /* #   ...\n\ */
+   int modcovmax =1;
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   int mobilavrange, mob;
+   double age;
-   for(itimes=1;itimes<=2;itimes++){
-     jj=0;
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-     for(i=1; i <=nlstate; i++){
+                            a covariate has 2 modalities */
-       for(j=1; j <=nlstate+ndeath; j++){
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-         if(j==i) continue;
-         for(k=1; k<=ncovmodel;k++){
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-           jj++;
+     if(mobilav==1) mobilavrange=5; /* default */
-           ca[0]= k+'a'-1;ca[1]='\0';
+     else mobilavrange=mobilav;
-           if(itimes==1){
+     for (age=bage; age<=fage; age++)
-             printf("#%1d%1d%d",i,j,k);
+       for (i=1; i<=nlstate;i++)
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           }else{
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-             printf("%1d%1d%d",i,j,k);
+     /* We keep the original values on the extreme ages bage, fage and for
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-             /*  printf(" %.5le",matcov[i][j]); */
+        we use a 5 terms etc. until the borders are no more concerned.
-           }
+     */
-           ll=0;
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-           for(li=1;li <=nlstate; li++){
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+         for (i=1; i<=nlstate;i++){
-               if(lj==li) continue;
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-               for(lk=1;lk<=ncovmodel;lk++){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-                 ll++;
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-                 if(ll<=jj){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-                   if(ll<jj){
+               }
-                     if(itimes==1){
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           }
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         }
-                     }else{
+       }/* end age */
-                       printf(" 0.");
+     }/* end mob */
-                       fprintf(ficparo," 0.");
+   }else return -1;
-                     }
+   return 0;
-                   }else{
+ }/* End movingaverage */
-                     if(itimes==1){
-                       printf(" Var(%s%1d%1d)",ca,i,j);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+ /************** Forecasting ******************/
-                     }else{
+ prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
-                       printf(" 0.");
+   /* proj1, year, month, day of starting projection
-                       fprintf(ficparo," 0.");
+      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).
-                 }
+   */
-               } /* end lk */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
-             } /* end lj */
+   double agec; /* generic age */
-           } /* end li */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-           printf("\n");
+   double *popeffectif,*popcount;
-           fprintf(ficparo,"\n");
+   double ***p3mat;
-           numlinepar++;
+   double ***mobaverage;
-         } /* end k*/
+   char fileresf[FILENAMELENGTH];
-       } /*end j */
-     } /* end i */
+   agelim=AGESUP;
-   } /* end itimes */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
- } /* end of prwizard */
+   strcpy(fileresf,"f");
- /******************* Gompertz Likelihood ******************************/
+   strcat(fileresf,fileres);
- double gompertz(double x[])
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
- {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-   double A,B,L=0.0,sump=0.,num=0.;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   int i,n=0; /* n is the size of the sample */
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   for (i=0;i<=imx-1 ; i++) {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-     sump=sump+weight[i];
-     /*    sump=sump+1;*/
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     num=num+1;
-   }
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   /* for (i=0; i<=imx; i++)
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-      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(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
-   for (i=1;i<=imx ; i++)
+   }
-     {
-       if (cens[i] == 1 && wav[i]>1)
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
-       if (cens[i] == 0 && wav[i]>1)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   }
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+   else  hstepm=estepm;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   hstepm=hstepm/stepm;
-       if (wav[i] > 1 ) { /* ??? */
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-         L=L+A*weight[i];
+                                fractional in yp1 */
-         /*      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]);*/
+   anprojmean=yp;
-       }
+   yp2=modf((yp1*12),&yp);
-     }
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
-   return -2*L*num/sump;
+   if(mprojmean==0) jprojmean=1;
- }
+   i1=cptcoveff;
- /******************* Printing html file ***********/
+   if (cptcovn < 1){i1=1;}
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-                   int lastpass, int stepm, int weightopt, char model[],\
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-                   int imx,  double p[],double **matcov,double agemortsup){
-   int i,k;
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+ /*            if (h==(int)(YEARM*yearp)){ */
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-   for (i=1;i<=2;i++)
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-     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]));
+       k=k+1;
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+       fprintf(ficresf,"\n#******");
-   fprintf(fichtm,"</ul>");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+       }
+       fprintf(ficresf,"******\n");
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+       for(j=1; j<=nlstate+ndeath;j++){
-  for (k=agegomp;k<(agemortsup-2);k++)
+         for(i=1; i<=nlstate;i++)
-    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+           fprintf(ficresf," p%d%d",i,j);
+         fprintf(ficresf," p.%d",j);
+       }
-   fflush(fichtm);
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
- }
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
- /******************* Gnuplot file **************/
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+         for (agec=fage; agec>=(ageminpar-1); agec--){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-   char dirfileres[132],optfileres[132];
+           nhstepm = nhstepm/hstepm;
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int ng;
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   /*#ifdef windows */
+           for (h=0; h<=nhstepm; h++){
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+             if (h*hstepm/YEARM*stepm ==yearp) {
-     /*#endif */
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   strcpy(dirfileres,optionfilefiname);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-   strcpy(optfileres,"vpl");
+             }
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+             for(j=1; j<=nlstate+ndeath;j++) {
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+               ppij=0.;
-   fprintf(ficgp, "set ter png small\n set log y\n");
+               for(i=1; i<=nlstate;i++) {
-   fprintf(ficgp, "set size 0.65,0.65\n");
+                 if (mobilav==1)
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                 else {
- }
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 }
+                 if (h*hstepm/YEARM*stepm== yearp) {
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                 }
+               } /* end i */
- /***********************************************/
+               if (h*hstepm/YEARM*stepm==yearp) {
- /**************** Main Program *****************/
+                 fprintf(ficresf," %.3f", ppij);
- /***********************************************/
+               }
+             }/* end j */
- int main(int argc, char *argv[])
+           } /* end h */
- {
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+         } /* end agec */
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+       } /* end yearp */
-   int linei, month, year,iout;
+     } /* end cptcod */
-   int jj, ll, li, lj, lk, imk;
+   } /* end  cptcov */
-   int numlinepar=0; /* Current linenumber of parameter file */
-   int itimes;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int NDIM=2;
+   fclose(ficresf);
-   char ca[32], cb[32], cc[32];
+ }
-   char dummy[]="                         ";
-   /*  FILE *fichtm; *//* Html File */
+ /************** Forecasting *****not tested NB*************/
-   /* FILE *ficgp;*/ /*Gnuplot File */
+ 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){
-   struct stat info;
-   double agedeb, agefin,hf;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   int *popage;
+   double calagedatem, agelim, kk1, kk2;
-   double fret;
+   double *popeffectif,*popcount;
-   double **xi,tmp,delta;
+   double ***p3mat,***tabpop,***tabpopprev;
+   double ***mobaverage;
-   double dum; /* Dummy variable */
+   char filerespop[FILENAMELENGTH];
-   double ***p3mat;
-   double ***mobaverage;
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int *indx;
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   char line[MAXLINE], linepar[MAXLINE];
+   agelim=AGESUP;
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
+   strcpy(filerespop,"pop");
-   int ju,jl, mi;
+   strcat(filerespop,fileres);
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   int mobilav=0,popforecast=0;
+   }
-   int hstepm, nhstepm;
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   int agemortsup;
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   float  sumlpop=0.;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   if (mobilav!=0) {
-   double bage, fage, age, agelim, agebase;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double ftolpl=FTOL;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   double **prlim;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   double *severity;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   double ***param; /* Matrix of parameters */
+     }
-   double  *p;
+   }
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   double *delti; /* Scale */
+   if (stepm<=12) stepsize=1;
-   double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
+   agelim=AGESUP;
-   double *epj, vepp;
-   double kk1, kk2;
+   hstepm=1;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   hstepm=hstepm/stepm;
-   double **ximort;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   if (popforecast==1) {
-   int *dcwave;
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   char z[1]="c", occ;
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+     }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+     popage=ivector(0,AGESUP);
-   char  *strt, strtend[80];
+     popeffectif=vector(0,AGESUP);
-   char *stratrunc;
+     popcount=vector(0,AGESUP);
-   int lstra;
+     i=1;
-   long total_usecs;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
- /*   setlocale (LC_ALL, ""); */
+     imx=i;
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
- /*   textdomain (PACKAGE); */
+   }
- /*   setlocale (LC_CTYPE, ""); */
- /*   setlocale (LC_MESSAGES, ""); */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       k=k+1;
-   (void) gettimeofday(&start_time,&tzp);
+       fprintf(ficrespop,"\n#******");
-   curr_time=start_time;
+       for(j=1;j<=cptcoveff;j++) {
-   tm = *localtime(&start_time.tv_sec);
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   tmg = *gmtime(&start_time.tv_sec);
+       }
-   strcpy(strstart,asctime(&tm));
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
- /*  printf("Localtime (at start)=%s",strstart); */
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- /*  tp.tv_sec = tp.tv_sec +86400; */
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
- /*  tm = *localtime(&start_time.tv_sec); */
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       for (cpt=0; cpt<=0;cpt++) {
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
- /*   tp.tv_sec = mktime(&tmg); */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- /*   strt=asctime(&tmg); */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- /*   printf("Time(after) =%s",strstart);  */
+           nhstepm = nhstepm/hstepm;
- /*  (void) time (&time_value);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- *  tm = *localtime(&time_value);
+           oldm=oldms;savm=savms;
- *  strstart=asctime(&tm);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
- */
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   nberr=0; /* Number of errors and warnings */
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   nbwarn=0;
+             }
-   getcwd(pathcd, size);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   printf("\n%s\n%s",version,fullversion);
+               for(i=1; i<=nlstate;i++) {
-   if(argc <=1){
+                 if (mobilav==1)
-     printf("\nEnter the parameter file name: ");
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-     fgets(pathr,FILENAMELENGTH,stdin);
+                 else {
-     i=strlen(pathr);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-     if(pathr[i-1]=='\n')
+                 }
-       pathr[i-1]='\0';
+               }
-    for (tok = pathr; tok != NULL; ){
+               if (h==(int)(calagedatem+12*cpt)){
-       printf("Pathr |%s|\n",pathr);
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+                   /*fprintf(ficrespop," %.3f", kk1);
-       printf("val= |%s| pathr=%s\n",val,pathr);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-       strcpy (pathtot, val);
+               }
-       if(pathr[0] == '\0') break; /* Dirty */
+             }
-     }
+             for(i=1; i<=nlstate;i++){
-   }
+               kk1=0.;
-   else{
+                 for(j=1; j<=nlstate;j++){
-     strcpy(pathtot,argv[1]);
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   }
+                 }
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   /*cygwin_split_path(pathtot,path,optionfile);
+             }
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   /* Split argv[0], imach program to get pathimach */
+           }
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+         }
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+       }
-  /*   strcpy(pathimach,argv[0]); */
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+   /******/
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   chdir(path); /* Can be a relative path */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-     printf("Current directory %s!\n",pathcd);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   strcpy(command,"mkdir ");
+           nhstepm = nhstepm/hstepm;
-   strcat(command,optionfilefiname);
-   if((outcmd=system(command)) != 0){
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+           oldm=oldms;savm=savms;
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     /* fclose(ficlog); */
+           for (h=0; h<=nhstepm; h++){
- /*     exit(1); */
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   }
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+             }
- /*     perror("mkdir"); */
+             for(j=1; j<=nlstate+ndeath;j++) {
- /*   } */
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
-   /*-------- arguments in the command line --------*/
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
-   /* Log file */
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   strcat(filelog, optionfilefiname);
+             }
-   strcat(filelog,".log");    /* */
+           }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("Problem with logfile %s\n",filelog);
+         }
-     goto end;
+       }
-   }
+    }
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+   }
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-  path=%s \n\
+   if (popforecast==1) {
-  optionfile=%s\n\
+     free_ivector(popage,0,AGESUP);
-  optionfilext=%s\n\
+     free_vector(popeffectif,0,AGESUP);
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+     free_vector(popcount,0,AGESUP);
+   }
-   printf("Local time (at start):%s",strstart);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fflush(ficlog);
+   fclose(ficrespop);
- /*   (void) gettimeofday(&curr_time,&tzp); */
+ } /* End of popforecast */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+ int fileappend(FILE *fichier, char *optionfich)
-   /* */
+ {
-   strcpy(fileres,"r");
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-   strcat(fileres, optionfilefiname);
+     printf("Problem with file: %s\n", optionfich);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
-   /*---------arguments file --------*/
+   }
+   fflush(fichier);
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+   return (1);
-     printf("Problem with optionfile %s\n",optionfile);
+ }
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-     fflush(ficlog);
-     goto end;
+ /**************** function prwizard **********************/
-   }
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+ {
+   /* Wizard to print covariance matrix template */
-   strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   char ca[32], cb[32];
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
-     printf("Problem with Output resultfile: %s\n", filereso);
+   int numlinepar;
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-     fflush(ficlog);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     goto end;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   }
+   for(i=1; i <=nlstate; i++){
+     jj=0;
-   /* Reads comments: lines beginning with '#' */
+     for(j=1; j <=nlstate+ndeath; j++){
-   numlinepar=0;
+       if(j==i) continue;
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       jj++;
-     ungetc(c,ficpar);
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-     fgets(line, MAXLINE, ficpar);
+       printf("%1d%1d",i,j);
-     numlinepar++;
+       fprintf(ficparo,"%1d%1d",i,j);
-     puts(line);
+       for(k=1; k<=ncovmodel;k++){
-     fputs(line,ficparo);
+         /*        printf(" %lf",param[i][j][k]); */
-     fputs(line,ficlog);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-   }
+         printf(" 0.");
-   ungetc(c,ficpar);
+         fprintf(ficparo," 0.");
+       }
-   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);
+       printf("\n");
-   numlinepar++;
+       fprintf(ficparo,"\n");
-   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);
+   printf("# Scales (for hessian or gradient estimation)\n");
-   fflush(ficlog);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   while((c=getc(ficpar))=='#' && c!= EOF){
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     ungetc(c,ficpar);
+   for(i=1; i <=nlstate; i++){
-     fgets(line, MAXLINE, ficpar);
+     jj=0;
-     numlinepar++;
+     for(j=1; j <=nlstate+ndeath; j++){
-     puts(line);
+       if(j==i) continue;
-     fputs(line,ficparo);
+       jj++;
-     fputs(line,ficlog);
+       fprintf(ficparo,"%1d%1d",i,j);
-   }
+       printf("%1d%1d",i,j);
-   ungetc(c,ficpar);
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
-   covar=matrix(0,NCOVMAX,1,n);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+         printf(" 0.");
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+         fprintf(ficparo," 0.");
+       }
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+       numlinepar++;
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       printf("\n");
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       fprintf(ficparo,"\n");
+     }
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   }
-   delti=delti3[1][1];
+   printf("# Covariance matrix\n");
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+ /* # 121 Var(a12)\n\ */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-     free_ma3x(delti3,1,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\ */
-     fclose (ficparo);
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-     fclose (ficlog);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-     goto end;
+   fflush(stdout);
-     exit(0);
+   fprintf(ficparo,"# Covariance matrix\n");
-   }
+   /* # 121 Var(a12)\n\ */
-   else if(mle==-3) {
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+   /* #   ...\n\ */
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   for(itimes=1;itimes<=2;itimes++){
-     matcov=matrix(1,npar,1,npar);
+     jj=0;
-   }
+     for(i=1; i <=nlstate; i++){
-   else{
+       for(j=1; j <=nlstate+ndeath; j++){
-     /* Read guess parameters */
+         if(j==i) continue;
-     /* Reads comments: lines beginning with '#' */
+         for(k=1; k<=ncovmodel;k++){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           jj++;
-       ungetc(c,ficpar);
+           ca[0]= k+'a'-1;ca[1]='\0';
-       fgets(line, MAXLINE, ficpar);
+           if(itimes==1){
-       numlinepar++;
+             printf("#%1d%1d%d",i,j,k);
-       puts(line);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-       fputs(line,ficparo);
+           }else{
-       fputs(line,ficlog);
+             printf("%1d%1d%d",i,j,k);
-     }
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-     ungetc(c,ficpar);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+           ll=0;
-     for(i=1; i <=nlstate; i++){
+           for(li=1;li <=nlstate; li++){
-       j=0;
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+               if(lj==li) continue;
-         if(jj==i) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
-         j++;
+                 ll++;
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+                 if(ll<=jj){
-         if ((i1 != i) && (j1 != j)){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+                   if(ll<jj){
- It might be a problem of design; if ncovcol and the model are correct\n \
+                     if(itimes==1){
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-           exit(1);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-         }
+                     }else{
-         fprintf(ficparo,"%1d%1d",i1,j1);
+                       printf(" 0.");
-         if(mle==1)
+                       fprintf(ficparo," 0.");
-           printf("%1d%1d",i,j);
+                     }
-         fprintf(ficlog,"%1d%1d",i,j);
+                   }else{
-         for(k=1; k<=ncovmodel;k++){
+                     if(itimes==1){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-           if(mle==1){
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-             printf(" %lf",param[i][j][k]);
+                     }else{
-             fprintf(ficlog," %lf",param[i][j][k]);
+                       printf(" 0.");
-           }
+                       fprintf(ficparo," 0.");
-           else
+                     }
-             fprintf(ficlog," %lf",param[i][j][k]);
+                   }
-           fprintf(ficparo," %lf",param[i][j][k]);
+                 }
-         }
+               } /* end lk */
-         fscanf(ficpar,"\n");
+             } /* end lj */
-         numlinepar++;
+           } /* end li */
-         if(mle==1)
+           printf("\n");
-           printf("\n");
+           fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+           numlinepar++;
-         fprintf(ficparo,"\n");
+         } /* end k*/
-       }
+       } /*end j */
-     }
+     } /* end i */
-     fflush(ficlog);
+   } /* end itimes */
-     p=param[1][1];
+ } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
-     /* Reads comments: lines beginning with '#' */
+ double gompertz(double x[])
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ {
-       ungetc(c,ficpar);
+   double A,B,L=0.0,sump=0.,num=0.;
-       fgets(line, MAXLINE, ficpar);
+   int i,n=0; /* n is the size of the sample */
-       numlinepar++;
-       puts(line);
+   for (i=0;i<=imx-1 ; i++) {
-       fputs(line,ficparo);
+     sump=sump+weight[i];
-       fputs(line,ficlog);
+     /*    sump=sump+1;*/
-     }
+     num=num+1;
-     ungetc(c,ficpar);
+   }
-     for(i=1; i <=nlstate; i++){
-       for(j=1; j <=nlstate+ndeath-1; j++){
+   /* for (i=0; i<=imx; i++)
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-         if ((i1-i)*(j1-j)!=0){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+   for (i=1;i<=imx ; i++)
-           exit(1);
+     {
-         }
+       if (cens[i] == 1 && wav[i]>1)
-         printf("%1d%1d",i,j);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       if (cens[i] == 0 && wav[i]>1)
-         for(k=1; k<=ncovmodel;k++){
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-           fprintf(ficlog," %le",delti3[i][j][k]);
+       if (wav[i] > 1 ) { /* ??? */
-         }
+         L=L+A*weight[i];
-         fscanf(ficpar,"\n");
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-         numlinepar++;
+       }
-         printf("\n");
+     }
-         fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       }
-     }
+   return -2*L*num/sump;
-     fflush(ficlog);
+ }
-     delti=delti3[1][1];
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
+ double gompertz_f(const gsl_vector *v, void *params)
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
-     /* Reads comments: lines beginning with '#' */
+   double *x= (double *) v->data;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   int i,n=0; /* n is the size of the sample */
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   for (i=0;i<=imx-1 ; i++) {
-       numlinepar++;
+     sump=sump+weight[i];
-       puts(line);
+     /*    sump=sump+1;*/
-       fputs(line,ficparo);
+     num=num+1;
-       fputs(line,ficlog);
+   }
-     }
-     ungetc(c,ficpar);
+   /* for (i=0; i<=imx; i++)
-     matcov=matrix(1,npar,1,npar);
+      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]);*/
-     for(i=1; i <=npar; i++){
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-       fscanf(ficpar,"%s",&str);
+   for (i=1;i<=imx ; i++)
-       if(mle==1)
+     {
-         printf("%s",str);
+       if (cens[i] == 1 && wav[i]>1)
-       fprintf(ficlog,"%s",str);
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       fprintf(ficparo,"%s",str);
-       for(j=1; j <=i; j++){
+       if (cens[i] == 0 && wav[i]>1)
-         fscanf(ficpar," %le",&matcov[i][j]);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-         if(mle==1){
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-           printf(" %.5le",matcov[i][j]);
-         }
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-         fprintf(ficlog," %.5le",matcov[i][j]);
+       if (wav[i] > 1 ) { /* ??? */
-         fprintf(ficparo," %.5le",matcov[i][j]);
+         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]);*/
-       fscanf(ficpar,"\n");
+       }
-       numlinepar++;
+     }
-       if(mle==1)
-         printf("\n");
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       fprintf(ficlog,"\n");
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-       fprintf(ficparo,"\n");
-     }
+   return -2*LL*num/sump;
-     for(i=1; i <=npar; i++)
+ }
-       for(j=i+1;j<=npar;j++)
+ #endif
-         matcov[i][j]=matcov[j][i];
+ /******************* Printing html file ***********/
-     if(mle==1)
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-       printf("\n");
+                   int lastpass, int stepm, int weightopt, char model[],\
-     fprintf(ficlog,"\n");
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
-     fflush(ficlog);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     /*-------- Rewriting parameter file ----------*/
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+   for (i=1;i<=2;i++)
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     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]));
-     strcat(rfileres,".");    /* */
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   fprintf(fichtm,"</ul>");
-     if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     }
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
-     fprintf(ficres,"#%s\n",version);
-   }    /* End of mle != -3 */
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+   fflush(fichtm);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+ }
-   }
+ /******************* Gnuplot file **************/
-   n= lastobs;
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
+   char dirfileres[132],optfileres[132];
-   num=lvector(1,n);
-   moisnais=vector(1,n);
+   int ng;
-   annais=vector(1,n);
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+   /*#ifdef windows */
-   agedc=vector(1,n);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   cod=ivector(1,n);
+     /*#endif */
-   weight=vector(1,n);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-   mint=matrix(1,maxwav,1,n);
+   strcpy(dirfileres,optionfilefiname);
-   anint=matrix(1,maxwav,1,n);
+   strcpy(optfileres,"vpl");
-   s=imatrix(1,maxwav+1,1,n);
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   tab=ivector(1,NCOVMAX);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   ncodemax=ivector(1,8);
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-   i=1;
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-   linei=0;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+ }
-     linei=linei+1;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-       if(line[j] == '\t')
+ {
-         line[j] = ' ';
-     }
+   /*-------- data file ----------*/
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   FILE *fic;
-       ;
+   char dummy[]="                         ";
-     };
+   int i=0, j=0, n=0;
-     line[j+1]=0;  /* Trims blanks at end of line */
+   int linei, month, year,iout;
-     if(line[0]=='#'){
+   char line[MAXLINE], linetmp[MAXLINE];
-       fprintf(ficlog,"Comment line\n%s\n",line);
+   char stra[MAXLINE], strb[MAXLINE];
-       printf("Comment line\n%s\n",line);
+   char *stratrunc;
-       continue;
+   int lstra;
-     }
-     for (j=maxwav;j>=1;j--){
+   if((fic=fopen(datafile,"r"))==NULL)    {
-       cutv(stra, strb,line,' ');
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-       errno=0;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       lval=strtol(strb,&endptr,10);
+   }
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   i=1;
-         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);
+   linei=0;
-         exit(1);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       }
+     linei=linei+1;
-       s[j][i]=lval;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       if(line[j] == '\t')
-       strcpy(line,stra);
+         line[j] = ' ';
-       cutv(stra, strb,line,' ');
+     }
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       }
+       ;
-       else  if(iout=sscanf(strb,"%s.") != 0){
+     };
-         month=99;
+     line[j+1]=0;  /* Trims blanks at end of line */
-         year=9999;
+     if(line[0]=='#'){
-       }else{
+       fprintf(ficlog,"Comment line\n%s\n",line);
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+       printf("Comment line\n%s\n",line);
-         exit(1);
+       continue;
-       }
+     }
-       anint[j][i]= (double) year;
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       mint[j][i]= (double)month;
+     strcpy(line, linetmp);
-       strcpy(line,stra);
-     } /* ENd Waves */
+     for (j=maxwav;j>=1;j--){
-     cutv(stra, strb,line,' ');
+       cutv(stra, strb, line, ' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       if(strb[0]=='.') { /* Missing status */
-     }
+         lval=-1;
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       }else{
-       month=99;
+         errno=0;
-       year=9999;
+         lval=strtol(strb,&endptr,10);
-     }else{
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       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);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-       exit(1);
+           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);
-     }
+           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);
-     andc[i]=(double) year;
+           return 1;
-     moisdc[i]=(double) month;
+         }
-     strcpy(line,stra);
+       }
+       s[j][i]=lval;
-     cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       strcpy(line,stra);
-     }
+       cutv(stra, strb,line,' ');
-     else  if(iout=sscanf(strb,"%s.") != 0){
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       month=99;
+       }
-       year=9999;
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     }else{
+         month=99;
-       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);
+         year=9999;
-       exit(1);
+       }else{
-     }
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     annais[i]=(double)(year);
+         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);
-     moisnais[i]=(double)(month);
+         return 1;
-     strcpy(line,stra);
+       }
+       anint[j][i]= (double) year;
-     cutv(stra, strb,line,' ');
+       mint[j][i]= (double)month;
-     errno=0;
+       strcpy(line,stra);
-     dval=strtod(strb,&endptr);
+     } /* ENd Waves */
-     if( strb[0]=='\0' || (*endptr != '\0')){
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+     cutv(stra, strb,line,' ');
-       exit(1);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
      }
-     weight[i]=dval;
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     strcpy(line,stra);
+       month=99;
+       year=9999;
-     for (j=ncovcol;j>=1;j--){
+     }else{
-       cutv(stra, strb,line,' ');
+       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);
-       errno=0;
+         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);
-       lval=strtol(strb,&endptr,10);
+         return 1;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     }
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+     andc[i]=(double) year;
-         exit(1);
+     moisdc[i]=(double) month;
-       }
+     strcpy(line,stra);
-       if(lval <-1 || lval >1){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+     cutv(stra, strb,line,' ');
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+     }
-  For example, for multinomial values like 1, 2 and 3,\n \
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-  build V1=0 V2=0 for the reference value (1),\n \
+       month=99;
-         V1=1 V2=0 for (2) \n \
+       year=9999;
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+     }else{
-  output of IMaCh is often meaningless.\n \
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-  Exiting.\n",lval,linei, i,line,j);
+       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);
-         exit(1);
+         return 1;
-       }
+     }
-       covar[j][i]=(double)(lval);
+     if (year==9999) {
-       strcpy(line,stra);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-     }
+       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);
-     lstra=strlen(stra);
+         return 1;
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+     }
-       stratrunc = &(stra[lstra-9]);
+     annais[i]=(double)(year);
-       num[i]=atol(stratrunc);
+     moisnais[i]=(double)(month);
-     }
+     strcpy(line,stra);
-     else
-       num[i]=atol(stra);
+     cutv(stra, strb,line,' ');
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+     errno=0;
-       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;}*/
+     dval=strtod(strb,&endptr);
+     if( strb[0]=='\0' || (*endptr != '\0')){
-     i=i+1;
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-   } /* End loop reading  data */
+       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);
-   fclose(fic);
+       fflush(ficlog);
-   /* printf("ii=%d", ij);
+       return 1;
-      scanf("%d",i);*/
+     }
-   imx=i-1; /* Number of individuals */
+     weight[i]=dval;
+     strcpy(line,stra);
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+     for (j=ncovcol;j>=1;j--){
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+       cutv(stra, strb,line,' ');
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+       if(strb[0]=='.') { /* Missing status */
-     }*/
+         lval=-1;
-    /*  for (i=1; i<=imx; i++){
+       }else{
-      if (s[4][i]==9)  s[4][i]=-1;
+         errno=0;
-      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]));}*/
+         lval=strtol(strb,&endptr,10);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   /* for (i=1; i<=imx; i++) */
+           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);
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+           return 1;
-      else weight[i]=1;*/
+         }
+       }
-   /* Calculation of the number of parameters from char model */
+       if(lval <-1 || lval >1){
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-   Tprod=ivector(1,15);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   Tvaraff=ivector(1,15);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-   Tvard=imatrix(1,15,1,2);
+  For example, for multinomial values like 1, 2 and 3,\n \
-   Tage=ivector(1,15);
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     j=0, j1=0, k1=1, k2=1;
+  output of IMaCh is often meaningless.\n \
-     j=nbocc(model,'+'); /* j=Number of '+' */
+  Exiting.\n",lval,linei, i,line,j);
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     cptcovn=j+1;
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     cptcovprod=j1; /*Number of products */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
-     strcpy(modelsav,model);
+  build V1=0 V2=0 for the reference value (1),\n \
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+         V1=1 V2=0 for (2) \n \
-       printf("Error. Non available option model=%s ",model);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+  output of IMaCh is often meaningless.\n \
-       goto end;
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-     }
+         return 1;
+       }
-     /* This loop fills the array Tvar from the string 'model'.*/
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
-     for(i=(j+1); i>=1;i--){
+     }
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+     lstra=strlen(stra);
-       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(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       /*scanf("%d",i);*/
+       stratrunc = &(stra[lstra-9]);
-       if (strchr(strb,'*')) {  /* Model includes a product */
+       num[i]=atol(stratrunc);
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+     }
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+     else
-           cptcovprod--;
+       num[i]=atol(stra);
-           cutv(strb,stre,strd,'V');
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+       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;}*/
-           cptcovage++;
-             Tage[cptcovage]=i;
+     i=i+1;
-             /*printf("stre=%s ", stre);*/
+   } /* End loop reading  data */
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+   *imax=i-1; /* Number of individuals */
-           cptcovprod--;
+   fclose(fic);
-           cutv(strb,stre,strc,'V');
-           Tvar[i]=atoi(stre);
+   return (0);
-           cptcovage++;
+   /* endread: */
-           Tage[cptcovage]=i;
+     printf("Exiting readdata: ");
-         }
+     fclose(fic);
-         else {  /* Age is not in the model */
+     return (1);
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
+ }
-           Tvard[k1][1]=atoi(strc); /* m*/
+ void removespace(char *str) {
-           Tvard[k1][2]=atoi(stre); /* n */
+   char *p1 = str, *p2 = str;
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+   do
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+     while (*p2 == ' ')
-           for (k=1; k<=lastobs;k++)
+       p2++;
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   while (*p1++ = *p2++);
-           k1++;
+ }
-           k2=k2+2;
-         }
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-       }
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-       else { /* no more sum */
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-        /*  scanf("%d",i);*/
+    * - cptcovage number of covariates with age*products =2
-       cutv(strd,strc,strb,'V');
+    * - cptcovs number of simple covariates
-       Tvar[i]=atoi(strc);
+    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
-       }
+    *     which is a new column after the 9 (ncovcol) variables.
-       strcpy(modelsav,stra);
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-         scanf("%d",i);*/
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-     } /* end of loop + */
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-   } /* end model */
+  */
+ {
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+   int i, j, k, ks;
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   int  j1, k1, k2;
+   char modelsav[80];
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-   printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-   scanf("%d ",i);*/
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-     /*  if(mle==1){*/
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-   if (weightopt != 1) { /* Maximisation without weights*/
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     for(i=1;i<=n;i++) weight[i]=1.0;
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-   }
+                   /* including age products which are counted in cptcovage.
-     /*-calculation of age at interview from date of interview and age at death -*/
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-   agev=matrix(1,maxwav,1,imx);
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-   for (i=1; i<=imx; i++) {
+     strcpy(modelsav,model);
-     for(m=2; (m<= maxwav); m++) {
+     if (strstr(model,"AGE") !=0){
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-         anint[m][i]=9999;
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-         s[m][i]=-1;
+       return 1;
-       }
+     }
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+     if (strstr(model,"v") !=0){
-         nberr++;
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-         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. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-         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);
+       return 1;
-         s[m][i]=-1;
+     }
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+     /*   Design
-         nberr++;
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-         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]);
+      *  <          ncovcol=8                >
-         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]);
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+      *   k=  1    2      3       4     5       6      7        8
-       }
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-     }
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-   }
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-   for (i=1; i<=imx; i++)  {
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+      *  Tage[++cptcovage]=k
-     for(m=firstpass; (m<= lastpass); m++){
+      *       if products, new covar are created after ncovcol with k1
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-         if (s[m][i] >= nlstate+1) {
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-           if(agedc[i]>0)
+      *  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
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-               agev[m][i]=agedc[i];
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-             else {
+      *  <          ncovcol=8                >
-               if ((int)andc[i]!=9999){
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-                 nbwarn++;
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+      * 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];
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+      *How to reorganize?
-                                  years but with the precision of a month */
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-             agev[m][i]=1;
+      * Struct []
-           else if(agev[m][i] <agemin){
+      */
-             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);*/
+     /* 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 */
-           else if(agev[m][i] >agemax){
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-             agemax=agev[m][i];
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-           }
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+     /*  k=1 Tvar[1]=2 (from V2) */
-           /*     agev[m][i] = age[i]+2*m;*/
+     /*  k=5 Tvar[5] */
-         }
+     /* for (k=1; k<=cptcovn;k++) { */
-         else { /* =9 */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-           agev[m][i]=1;
+     /*  } */
-           s[m][i]=-1;
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-         }
+     /*
-       }
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-       else /*= 0 Unknown */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-         agev[m][i]=1;
+         Tvar[k]=0;
-     }
+     cptcovage=0;
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-   }
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-   for (i=1; i<=imx; i++)  {
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-     for(m=firstpass; (m<=lastpass); m++){
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-       if (s[m][i] > (nlstate+ndeath)) {
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-         nberr++;
+       /*scanf("%d",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);
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-         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);
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         goto end;
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-       }
+           /* covar is not filled and then is empty */
-     }
+           cptcovprod--;
-   }
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-   /*for (i=1; i<=imx; i++){
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-   for (m=firstpass; (m<lastpass); m++){
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+           /*printf("stre=%s ", stre);*/
- }
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           cptcovprod--;
- }*/
+           cutl(stre,strb,strc,'V');
+           Tvar[k]=atoi(stre);
+           cptcovage++;
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           Tage[cptcovage]=k;
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+         } 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 */
-   agegomp=(int)agemin;
+           cptcovn++;
-   free_vector(severity,1,maxwav);
+           cptcovprodnoage++;k1++;
-   free_imatrix(outcome,1,maxwav+1,1,n);
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   free_vector(moisnais,1,n);
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-   free_vector(annais,1,n);
+                                   because this model-covariate is a construction we invent a new column
-   /* free_matrix(mint,1,maxwav,1,n);
+                                   ncovcol + k1
-      free_matrix(anint,1,maxwav,1,n);*/
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-   free_vector(moisdc,1,n);
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-   free_vector(andc,1,n);
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-   wav=ivector(1,imx);
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+           k2=k2+2;
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+           for (i=1; i<=lastobs;i++){
-   /* Concatenates waves */
+             /* Computes the new covariate which is a product of
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+           }
+         } /* End age is not in the model */
-   Tcode=ivector(1,100);
+       } /* End if model includes a product */
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+       else { /* no more sum */
-   ncodemax[1]=1;
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+        /*  scanf("%d",i);*/
+         cutl(strd,strc,strb,'V');
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+         ks++; /**< Number of simple covariates */
-                                  the estimations*/
+         cptcovn++;
-   h=0;
+         Tvar[k]=atoi(strd);
-   m=pow(2,cptcoveff);
+       }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   for(k=1;k<=cptcoveff; k++){
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-     for(i=1; i <=(m/pow(2,k));i++){
+         scanf("%d",i);*/
-       for(j=1; j <= ncodemax[k]; j++){
+     } /* end of loop + */
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   } /* end model */
-           h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+     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);
-   }
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-      codtab[1][2]=1;codtab[2][2]=2; */
+   scanf("%d ",i);*/
-   /* 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);
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-      }
+   /*endread:*/
-      printf("\n");
+     printf("Exiting decodemodel: ");
-      }
+     return (1);
-      scanf("%d",i);*/
+ }
-   /*------------ gnuplot -------------*/
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-   strcpy(optionfilegnuplot,optionfilefiname);
+ {
-   if(mle==-3)
+   int i, m;
-     strcat(optionfilegnuplot,"-mort");
-   strcat(optionfilegnuplot,".gp");
+   for (i=1; i<=imx; i++) {
+     for(m=2; (m<= maxwav); m++) {
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-     printf("Problem with file %s",optionfilegnuplot);
+         anint[m][i]=9999;
-   }
+         s[m][i]=-1;
-   else{
+       }
-     fprintf(ficgp,"\n# %s\n", version);
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+         *nberr++;
-     fprintf(ficgp,"set missing 'NaNq'\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\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);
-   /*  fclose(ficgp);*/
+         s[m][i]=-1;
-   /*--------- index.htm --------*/
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+         *nberr++;
-   if(mle==-3)
+         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]);
-     strcat(optionfilehtm,"-mort");
+         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]);
-   strcat(optionfilehtm,".htm");
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+       }
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     }
    }
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   for (i=1; i<=imx; i++)  {
-   strcat(optionfilehtmcov,"-cov.htm");
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     for(m=firstpass; (m<= lastpass); m++){
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-   }
+         if (s[m][i] >= nlstate+1) {
-   else{
+           if(agedc[i]>0)
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+               agev[m][i]=agedc[i];
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+             else {
-   }
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+                 agev[m][i]=-1;
- \n\
+               }
- <hr  size=\"2\" color=\"#EC5E5E\">\
+             }
-  <ul><li><h4>Parameter files</h4>\n\
+         }
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+                                  years but with the precision of a month */
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-  - Date and time at start: %s</ul>\n",\
+             agev[m][i]=1;
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           else if(agev[m][i] < *agemin){
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+             *agemin=agev[m][i];
-           fileres,fileres,\
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+           }
-   fflush(fichtm);
+           else if(agev[m][i] >*agemax){
+             *agemax=agev[m][i];
-   strcpy(pathr,path);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-   strcat(pathr,optionfilefiname);
+           }
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+         }
-      and prints on file fileres'p'. */
+         else { /* =9 */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+           agev[m][i]=1;
+           s[m][i]=-1;
-   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\
+       else /*= 0 Unknown */
- 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 */
+   }
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   for (i=1; i<=imx; i++)  {
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     for(m=firstpass; (m<=lastpass); m++){
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+       if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-   /* For Powell, parameters are in a vector p[] starting at p[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);
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+         return 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){
+   /*for (i=1; i<=imx; i++){
-     ximort=matrix(1,NDIM,1,NDIM);
+   for (m=firstpass; (m<lastpass); m++){
-     cens=ivector(1,n);
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-     ageexmed=vector(1,n);
+ }
-     agecens=vector(1,n);
-     dcwave=ivector(1,n);
+ }*/
-     for (i=1; i<=imx; i++){
-       dcwave[i]=-1;
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-       for (m=firstpass; m<=lastpass; m++)
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         if (s[m][i]>nlstate) {
-           dcwave[i]=m;
+   return (0);
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+  /* endread:*/
-           break;
+     printf("Exiting calandcheckages: ");
-         }
+     return (1);
-     }
+ }
-     for (i=1; i<=imx; i++) {
-       if (wav[i]>0){
+ /***********************************************/
-         ageexmed[i]=agev[mw[1][i]][i];
+ /**************** Main Program *****************/
-         j=wav[i];
+ /***********************************************/
-         agecens[i]=1.;
+ int main(int argc, char *argv[])
-         if (ageexmed[i]> 1 && wav[i] > 0){
+ {
-           agecens[i]=agev[mw[j][i]][i];
+ #ifdef GSL
-           cens[i]= 1;
+   const gsl_multimin_fminimizer_type *T;
-         }else if (ageexmed[i]< 1)
+   size_t iteri = 0, it;
-           cens[i]= -1;
+   int rval = GSL_CONTINUE;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   int status = GSL_SUCCESS;
-           cens[i]=0 ;
+   double ssval;
-       }
+ #endif
-       else cens[i]=-1;
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-     }
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-     for (i=1;i<=NDIM;i++) {
+   int jj, ll, li, lj, lk;
-       for (j=1;j<=NDIM;j++)
+   int numlinepar=0; /* Current linenumber of parameter file */
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   int itimes;
-     }
+   int NDIM=2;
+   int vpopbased=0;
-     p[1]=0.0268; p[NDIM]=0.083;
-     /*printf("%lf %lf", p[1], p[2]);*/
+   char ca[32], cb[32];
+   /*  FILE *fichtm; *//* Html File */
+   /* FILE *ficgp;*/ /*Gnuplot File */
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   struct stat info;
-     strcpy(filerespow,"pow-mort");
+   double agedeb;
-     strcat(filerespow,fileres);
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-       printf("Problem with resultfile: %s\n", filerespow);
+   double fret;
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   double dum; /* Dummy variable */
-     }
+   double ***p3mat;
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   double ***mobaverage;
-     /*  for (i=1;i<=nlstate;i++)
-         for(j=1;j<=nlstate+ndeath;j++)
+   char line[MAXLINE];
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     */
+   char pathr[MAXLINE], pathimach[MAXLINE];
-     fprintf(ficrespow,"\n");
+   char *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+   int c,  h , cpt;
-     fclose(ficrespow);
+   int jl;
+   int i1, j1, jk, stepsize;
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   int *tab;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     for(i=1; i <=NDIM; i++)
+   int mobilav=0,popforecast=0;
-       for(j=i+1;j<=NDIM;j++)
+   int hstepm, nhstepm;
-         matcov[i][j]=matcov[j][i];
+   int agemortsup;
+   float  sumlpop=0.;
-     printf("\nCovariance matrix\n ");
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     for(i=1; i <=NDIM; i++) {
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-       for(j=1;j<=NDIM;j++){
-         printf("%f ",matcov[i][j]);
+   double bage=0, fage=110, age, agelim, agebase;
-       }
+   double ftolpl=FTOL;
-       printf("\n ");
+   double **prlim;
-     }
+   double ***param; /* Matrix of parameters */
+   double  *p;
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+   double **matcov; /* Matrix of covariance */
-     for (i=1;i<=NDIM;i++)
+   double ***delti3; /* Scale */
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
-     lsurv=vector(1,AGESUP);
+   double **varpl; /* Variances of prevalence limits by age */
-     lpop=vector(1,AGESUP);
+   double *epj, vepp;
-     tpop=vector(1,AGESUP);
-     lsurv[agegomp]=100000;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
-     for (k=agegomp;k<=AGESUP;k++) {
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-       agemortsup=k;
+   int *dcwave;
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     }
+   char z[1]="c";
-     for (k=agegomp;k<agemortsup;k++)
+   /*char  *strt;*/
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   char strtend[80];
-     for (k=agegomp;k<agemortsup;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+ /*   setlocale (LC_ALL, ""); */
-       sumlpop=sumlpop+lpop[k];
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     }
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
-     tpop[agegomp]=sumlpop;
+ /*   setlocale (LC_MESSAGES, ""); */
-     for (k=agegomp;k<(agemortsup-3);k++){
-       /*  tpop[k+1]=2;*/
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-       tpop[k+1]=tpop[k]-lpop[k];
+   rstart_time = time(NULL);
-     }
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
+   curr_time=start_time;
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   /*tml = *localtime(&start_time.tm_sec);*/
-     for (k=agegomp;k<(agemortsup-2);k++)
+   /* strcpy(strstart,asctime(&tml)); */
-       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]);
+   strcpy(strstart,asctime(&start_time));
+ /*  printf("Localtime (at start)=%s",strstart); */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ /*  tm = *localtime(&start_time.tm_sec); */
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-                      stepm, weightopt,\
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-                      model,imx,p,matcov,agemortsup);
+ /*   tp.tm_sec = mktime(&tmg); */
+ /*   strt=asctime(&tmg); */
-     free_vector(lsurv,1,AGESUP);
+ /*   printf("Time(after) =%s",strstart);  */
-     free_vector(lpop,1,AGESUP);
+ /*  (void) time (&time_value);
-     free_vector(tpop,1,AGESUP);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-   } /* Endof if mle==-3 */
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
-   else{ /* For mle >=1 */
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+ */
-     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);
+   nberr=0; /* Number of errors and warnings */
-     for (k=1; k<=npar;k++)
+   nbwarn=0;
-       printf(" %d %8.5f",k,p[k]);
+   getcwd(pathcd, size);
-     printf("\n");
-     globpr=1; /* to print the contributions */
+   printf("\n%s\n%s",version,fullversion);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   if(argc <=1){
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     printf("\nEnter the parameter file name: ");
-     for (k=1; k<=npar;k++)
+     fgets(pathr,FILENAMELENGTH,stdin);
-       printf(" %d %8.5f",k,p[k]);
+     i=strlen(pathr);
-     printf("\n");
+     if(pathr[i-1]=='\n')
-     if(mle>=1){ /* Could be 1 or 2 */
+       pathr[i-1]='\0';
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     i=strlen(pathr);
-     }
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
-     /*--------- results files --------------*/
+    for (tok = pathr; tok != NULL; ){
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+       printf("val= |%s| pathr=%s\n",val,pathr);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       strcpy (pathtot, val);
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       if(pathr[0] == '\0') break; /* Dirty */
-     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++){
+   else{
-         if (k != i) {
+     strcpy(pathtot,argv[1]);
-           printf("%d%d ",i,k);
+   }
-           fprintf(ficlog,"%d%d ",i,k);
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-           fprintf(ficres,"%1d%1d ",i,k);
+   /*cygwin_split_path(pathtot,path,optionfile);
-           for(j=1; j <=ncovmodel; j++){
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-             printf("%lf ",p[jk]);
+   /* cutv(path,optionfile,pathtot,'\\');*/
-             fprintf(ficlog,"%lf ",p[jk]);
-             fprintf(ficres,"%lf ",p[jk]);
+   /* Split argv[0], imach program to get pathimach */
-             jk++;
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-           }
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           printf("\n");
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           fprintf(ficlog,"\n");
+  /*   strcpy(pathimach,argv[0]); */
-           fprintf(ficres,"\n");
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-         }
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-       }
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-     }
+   chdir(path); /* Can be a relative path */
-     if(mle!=0){
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-       /* Computing hessian and covariance matrix */
+     printf("Current directory %s!\n",pathcd);
-       ftolhess=ftol; /* Usually correct */
+   strcpy(command,"mkdir ");
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+   strcat(command,optionfilefiname);
-     }
+   if((outcmd=system(command)) != 0){
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     printf("# Scales (for hessian or gradient estimation)\n");
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     /* fclose(ficlog); */
-     for(i=1,jk=1; i <=nlstate; i++){
+ /*     exit(1); */
-       for(j=1; j <=nlstate+ndeath; j++){
+   }
-         if (j!=i) {
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-           fprintf(ficres,"%1d%1d",i,j);
+ /*     perror("mkdir"); */
-           printf("%1d%1d",i,j);
+ /*   } */
-           fprintf(ficlog,"%1d%1d",i,j);
-           for(k=1; k<=ncovmodel;k++){
+   /*-------- arguments in the command line --------*/
-             printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
+   /* Log file */
-             fprintf(ficres," %.5e",delti[jk]);
+   strcat(filelog, optionfilefiname);
-             jk++;
+   strcat(filelog,".log");    /* */
-           }
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-           printf("\n");
+     printf("Problem with logfile %s\n",filelog);
-           fprintf(ficlog,"\n");
+     goto end;
-           fprintf(ficres,"\n");
+   }
-         }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-       }
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-     }
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\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");
+  path=%s \n\
-     if(mle>=1)
+  optionfile=%s\n\
-       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");
+  optionfilext=%s\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");
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     /* # 121 Var(a12)\n\ */
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   printf("Local time (at start):%s",strstart);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   fflush(ficlog);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     /* # 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" */
+   /* */
+   strcpy(fileres,"r");
+   strcat(fileres, optionfilefiname);
-     /* Just to have a covariance matrix which will be more understandable
+   strcat(fileres,".txt");    /* Other files have txt extension */
-        even is we still don't want to manage dictionary of variables
-     */
+   /*---------arguments file --------*/
-     for(itimes=1;itimes<=2;itimes++){
-       jj=0;
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-       for(i=1; i <=nlstate; i++){
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-         for(j=1; j <=nlstate+ndeath; j++){
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-           if(j==i) continue;
+     fflush(ficlog);
-           for(k=1; k<=ncovmodel;k++){
+     /* goto end; */
-             jj++;
+     exit(70);
-             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);
+   strcpy(filereso,"o");
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+   strcat(filereso,fileres);
-             }else{
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-               if(mle>=1)
+     printf("Problem with Output resultfile: %s\n", filereso);
-                 printf("%1d%1d%d",i,j,k);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+     fflush(ficlog);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+     goto end;
-             }
+   }
-             ll=0;
-             for(li=1;li <=nlstate; li++){
+   /* Reads comments: lines beginning with '#' */
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+   numlinepar=0;
-                 if(lj==li) continue;
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                 for(lk=1;lk<=ncovmodel;lk++){
+     ungetc(c,ficpar);
-                   ll++;
+     fgets(line, MAXLINE, ficpar);
-                   if(ll<=jj){
+     numlinepar++;
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+     fputs(line,stdout);
-                     if(ll<jj){
+     fputs(line,ficparo);
-                       if(itimes==1){
+     fputs(line,ficlog);
-                         if(mle>=1)
+   }
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   ungetc(c,ficpar);
-                         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);
+   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);
-                       }else{
+   numlinepar++;
-                         if(mle>=1)
+   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);
-                           printf(" %.5e",matcov[jj][ll]);
+   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," %.5e",matcov[jj][ll]);
+   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(ficres," %.5e",matcov[jj][ll]);
+   fflush(ficlog);
-                       }
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                     }else{
+     ungetc(c,ficpar);
-                       if(itimes==1){
+     fgets(line, MAXLINE, ficpar);
-                         if(mle>=1)
+     numlinepar++;
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+     fputs(line, stdout);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+     //puts(line);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     fputs(line,ficparo);
-                       }else{
+     fputs(line,ficlog);
-                         if(mle>=1)
+   }
-                           printf(" %.5e",matcov[jj][ll]);
+   ungetc(c,ficpar);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-                     }
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-                   }
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-                 } /* end lk */
+      v1+v2*age+v2*v3 makes cptcovn = 3
-               } /* end lj */
+   */
-             } /* end li */
+   if (strlen(model)>1)
-             if(mle>=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*/
-               printf("\n");
+   else
-             fprintf(ficlog,"\n");
+     ncovmodel=2;
-             fprintf(ficres,"\n");
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-             numlinepar++;
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-           } /* end k*/
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-         } /*end j */
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-       } /* end i */
+     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);
-     } /* end itimes */
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
-     fflush(ficlog);
+     fclose (ficlog);
-     fflush(ficres);
+     goto end;
+   }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       ungetc(c,ficpar);
+   delti=delti3[1][1];
-       fgets(line, MAXLINE, ficpar);
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-       puts(line);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-       fputs(line,ficparo);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     }
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     ungetc(c,ficpar);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     estepm=0;
+     fclose (ficparo);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     fclose (ficlog);
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+     goto end;
-     if (fage <= 2) {
+     exit(0);
-       bage = ageminpar;
+   }
-       fage = agemaxpar;
+   else if(mle==-3) {
-     }
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     matcov=matrix(1,npar,1,npar);
+   }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   else{
-       ungetc(c,ficpar);
+     /* Read guessed parameters */
-       fgets(line, MAXLINE, ficpar);
+     /* Reads comments: lines beginning with '#' */
-       puts(line);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       fputs(line,ficparo);
+       ungetc(c,ficpar);
-     }
+       fgets(line, MAXLINE, ficpar);
-     ungetc(c,ficpar);
+       numlinepar++;
+       fputs(line,stdout);
-     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);
+       fputs(line,ficparo);
-     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);
+       fputs(line,ficlog);
-     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);
+     ungetc(c,ficpar);
-     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);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     for(i=1; i <=nlstate; i++){
-       ungetc(c,ficpar);
+       j=0;
-       fgets(line, MAXLINE, ficpar);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-       puts(line);
+         if(jj==i) continue;
-       fputs(line,ficparo);
+         j++;
-     }
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     ungetc(c,ficpar);
+         if ((i1 != i) && (j1 != j)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ It might be a problem of design; if ncovcol and the model are correct\n \
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+           exit(1);
+         }
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+         if(mle==1)
-     fprintf(ficres,"pop_based=%d\n",popbased);
+           printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         for(k=1; k<=ncovmodel;k++){
-       ungetc(c,ficpar);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-       fgets(line, MAXLINE, ficpar);
+           if(mle==1){
-       puts(line);
+             printf(" %lf",param[i][j][k]);
-       fputs(line,ficparo);
+             fprintf(ficlog," %lf",param[i][j][k]);
-     }
+           }
-     ungetc(c,ficpar);
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
-     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," %lf",param[i][j][k]);
-     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);
+         fscanf(ficpar,"\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);
+         numlinepar++;
-     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);
+         if(mle==1)
-     /* day and month of proj2 are not used but only year anproj2.*/
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     }
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     fflush(ficlog);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     /* Reads scales values */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     p=param[1][1];
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     /* Reads comments: lines beginning with '#' */
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+     while((c=getc(ficpar))=='#' && c!= EOF){
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-    /*------------ free_vector  -------------*/
+       numlinepar++;
-    /*  chdir(path); */
+       fputs(line,stdout);
+       fputs(line,ficparo);
-     free_ivector(wav,1,imx);
+       fputs(line,ficlog);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     }
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     ungetc(c,ficpar);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     free_lvector(num,1,n);
+     for(i=1; i <=nlstate; i++){
-     free_vector(agedc,1,n);
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+         if ( (i1-i) * (j1-j) != 0){
-     fclose(ficparo);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     fclose(ficres);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     strcpy(filerespl,"pl");
+         for(k=1; k<=ncovmodel;k++){
-     strcat(filerespl,fileres);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+           printf(" %le",delti3[i][j][k]);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+           fprintf(ficparo," %le",delti3[i][j][k]);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     }
+         }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+         fscanf(ficpar,"\n");
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+         numlinepar++;
-     pstamp(ficrespl);
+         printf("\n");
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+         fprintf(ficparo,"\n");
-     fprintf(ficrespl,"#Age ");
+         fprintf(ficlog,"\n");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+       }
-     fprintf(ficrespl,"\n");
+     }
+     fflush(ficlog);
-     prlim=matrix(1,nlstate,1,nlstate);
+     /* Reads covariance matrix */
-     agebase=ageminpar;
+     delti=delti3[1][1];
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
-     i1=cptcoveff;
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-     if (cptcovn < 1){i1=1;}
+     /* Reads comments: lines beginning with '#' */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       ungetc(c,ficpar);
-         k=k+1;
+       fgets(line, MAXLINE, ficpar);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+       numlinepar++;
-         fprintf(ficrespl,"\n#******");
+       fputs(line,stdout);
-         printf("\n#******");
+       fputs(line,ficparo);
-         fprintf(ficlog,"\n#******");
+       fputs(line,ficlog);
-         for(j=1;j<=cptcoveff;j++) {
+     }
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     ungetc(c,ficpar);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     matcov=matrix(1,npar,1,npar);
-         }
+     for(i=1; i <=npar; i++)
-         fprintf(ficrespl,"******\n");
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-         printf("******\n");
-         fprintf(ficlog,"******\n");
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
-         for (age=agebase; age<=agelim; age++){
+       if(mle==1)
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         printf("%s",str);
-           fprintf(ficrespl,"%.0f ",age );
+       fprintf(ficlog,"%s",str);
-           for(j=1;j<=cptcoveff;j++)
+       fprintf(ficparo,"%s",str);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for(j=1; j <=i; j++){
-           for(i=1; i<=nlstate;i++)
+         fscanf(ficpar," %le",&matcov[i][j]);
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+         if(mle==1){
-           fprintf(ficrespl,"\n");
+           printf(" %.5le",matcov[i][j]);
          }
-       }
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     }
+         fprintf(ficparo," %.5le",matcov[i][j]);
-     fclose(ficrespl);
+       }
+       fscanf(ficpar,"\n");
-     /*------------- h Pij x at various ages ------------*/
+       numlinepar++;
+       if(mle==1)
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+         printf("\n");
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       fprintf(ficlog,"\n");
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficparo,"\n");
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     }
-     }
+     for(i=1; i <=npar; i++)
-     printf("Computing pij: result on file '%s' \n", filerespij);
+       for(j=i+1;j<=npar;j++)
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+         matcov[i][j]=matcov[j][i];
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     if(mle==1)
-     /*if (stepm<=24) stepsize=2;*/
+       printf("\n");
+     fprintf(ficlog,"\n");
-     agelim=AGESUP;
-     hstepm=stepsize*YEARM; /* Every year of age */
+     fflush(ficlog);
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /*-------- Rewriting parameter file ----------*/
-     /* hstepm=1;   aff par mois*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     pstamp(ficrespij);
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     strcat(rfileres,".");    /* */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-         k=k+1;
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-         fprintf(ficrespij,"\n#****** ");
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-         for(j=1;j<=cptcoveff;j++)
+     }
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fprintf(ficres,"#%s\n",version);
-         fprintf(ficrespij,"******\n");
+   }    /* End of mle != -3 */
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   n= lastobs;
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   num=lvector(1,n);
+   moisnais=vector(1,n);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   annais=vector(1,n);
+   moisdc=vector(1,n);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   andc=vector(1,n);
-           oldm=oldms;savm=savms;
+   agedc=vector(1,n);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   cod=ivector(1,n);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+   weight=vector(1,n);
-           for(i=1; i<=nlstate;i++)
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-             for(j=1; j<=nlstate+ndeath;j++)
+   mint=matrix(1,maxwav,1,n);
-               fprintf(ficrespij," %1d-%1d",i,j);
+   anint=matrix(1,maxwav,1,n);
-           fprintf(ficrespij,"\n");
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-           for (h=0; h<=nhstepm; h++){
+   tab=ivector(1,NCOVMAX);
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
+   /* Reads data from file datafile */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-             fprintf(ficrespij,"\n");
+     goto end;
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* Calculation of the number of parameters from char model */
-           fprintf(ficrespij,"\n");
+     /*    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)
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-     fclose(ficrespij);
+   /*  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,
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
-     for(i=1;i<=AGESUP;i++)
+   */
-       for(j=1;j<=NCOVMAX;j++)
+   /* For model-covariate k tells which data-covariate to use but
-         for(k=1;k<=NCOVMAX;k++)
+     because this model-covariate is a construction we invent a new column
-           probs[i][j][k]=0.;
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     /*---------- Forecasting ------------------*/
+     Tvar[3=V1*V4]=4+1 etc */
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-     if(prevfcast==1){
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-       /*    if(stepm ==1){*/
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-       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);*/
+   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
-       /*      else{ */
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-       /*        erreur=108; */
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-       /*        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); */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-       /*        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); */
+covariates (3 plus signs)
-       /*      } */
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-     }
+                       */
+   if(decodemodel(model, lastobs) == 1)
-     /*---------- Health expectancies and variances ------------*/
+     goto end;
-     strcpy(filerest,"t");
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-     strcat(filerest,fileres);
+     nbwarn++;
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+     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);
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     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);
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   }
-     }
+     /*  if(mle==1){*/
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
-     strcpy(filerese,"e");
+     /*-calculation of age at interview from date of interview and age at death -*/
-     strcat(filerese,fileres);
+   agev=matrix(1,maxwav,1,imx);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     goto end;
-     }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   agegomp=(int)agemin;
+   free_vector(moisnais,1,n);
-     strcpy(fileresstde,"stde");
+   free_vector(annais,1,n);
-     strcat(fileresstde,fileres);
+   /* free_matrix(mint,1,maxwav,1,n);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+      free_matrix(anint,1,maxwav,1,n);*/
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   free_vector(moisdc,1,n);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   free_vector(andc,1,n);
-     }
+   /* */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   wav=ivector(1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     strcpy(filerescve,"cve");
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-     strcat(filerescve,fileres);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   /* Concatenates waves */
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     }
+   /* */
-     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);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     strcpy(fileresv,"v");
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-     strcat(fileresv,fileres);
+   ncodemax[1]=1;
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   Ndum =ivector(-1,NCOVMAX);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+   if (ncovmodel > 2)
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-     }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
+   h=0;
-     /* 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",\
+   /*if (cptcovn > 0) */
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
+   m=pow(2,cptcoveff);
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     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 */
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         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;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+            *     h     1     2     3     4
-         k=k+1;
+            *______________________________
-         fprintf(ficrest,"\n#****** ");
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-         for(j=1;j<=cptcoveff;j++)
+            *     2     2     1     1     1
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     3 i=2 1     2     1     1
-         fprintf(ficrest,"******\n");
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
-         fprintf(ficreseij,"\n#****** ");
+            *     6     2     1     2     1
-         fprintf(ficresstdeij,"\n#****** ");
+            *     7 i=4 1     2     2     1
-         fprintf(ficrescveij,"\n#****** ");
+            *     8     2     2     2     1
-         for(j=1;j<=cptcoveff;j++) {
+            *     9 i=5 1 i=3 1 i=2 1     1
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    10     2     1     1     1
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    11 i=6 1     2     1     1
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    12     2     2     1     1
-         }
+            *    13 i=7 1 i=4 1     2     1
-         fprintf(ficreseij,"******\n");
+            *    14     2     1     2     1
-         fprintf(ficresstdeij,"******\n");
+            *    15 i=8 1     2     2     1
-         fprintf(ficrescveij,"******\n");
+            *    16     2     2     2     1
+            */
-         fprintf(ficresvij,"\n#****** ");
+           codtab[h][k]=j;
-         for(j=1;j<=cptcoveff;j++)
+           /*codtab[h][Tvar[k]]=j;*/
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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]]);
-         fprintf(ficresvij,"******\n");
+         }
+       }
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     }
-         oldm=oldms;savm=savms;
+   }
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+      codtab[1][2]=1;codtab[2][2]=2; */
+   /* for(i=1; i <=m ;i++){
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+      for(k=1; k <=cptcovn; k++){
-         oldm=oldms;savm=savms;
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+      }
-         if(popbased==1){
+      printf("\n");
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+      }
-         }
+      scanf("%d",i);*/
-         pstamp(ficrest);
+  free_ivector(Ndum,-1,NCOVMAX);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-         fprintf(ficrest,"\n");
+   /*------------ gnuplot -------------*/
-         epj=vector(1,nlstate+1);
+   strcpy(optionfilegnuplot,optionfilefiname);
-         for(age=bage; age <=fage ;age++){
+   if(mle==-3)
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     strcat(optionfilegnuplot,"-mort");
-           if (popbased==1) {
+   strcat(optionfilegnuplot,".gp");
-             if(mobilav ==0){
-               for(i=1; i<=nlstate;i++)
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-                 prlim[i][i]=probs[(int)age][i][k];
+     printf("Problem with file %s",optionfilegnuplot);
-             }else{ /* mobilav */
+   }
-               for(i=1; i<=nlstate;i++)
+   else{
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     fprintf(ficgp,"\n# %s\n", version);
-             }
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-           }
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-           fprintf(ficrest," %4.0f",age);
+   }
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+   /*  fclose(ficgp);*/
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   /*--------- index.htm --------*/
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-             }
+   if(mle==-3)
-             epj[nlstate+1] +=epj[j];
+     strcat(optionfilehtm,"-mort");
-           }
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-           for(i=1, vepp=0.;i <=nlstate;i++)
+     printf("Problem with %s \n",optionfilehtm);
-             for(j=1;j <=nlstate;j++)
+     exit(0);
-               vepp += vareij[i][j][(int)age];
+   }
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-           for(j=1;j <=nlstate;j++){
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+   strcat(optionfilehtmcov,"-cov.htm");
-           }
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-           fprintf(ficrest,"\n");
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-         }
+   }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   else{
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-         free_vector(epj,1,nlstate+1);
+ <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);
-     free_vector(weight,1,n);
+   }
-     free_imatrix(Tvard,1,15,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     free_matrix(anint,1,maxwav,1,n);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     free_matrix(mint,1,maxwav,1,n);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     free_ivector(cod,1,n);
+ \n\
-     free_ivector(tab,1,NCOVMAX);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-     fclose(ficreseij);
+  <ul><li><h4>Parameter files</h4>\n\
-     fclose(ficresstdeij);
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-     fclose(ficrescveij);
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-     fclose(ficresvij);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     fclose(ficrest);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-     fclose(ficpar);
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     /*------- Variance of period (stable) prevalence------*/
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
-     strcpy(fileresvpl,"vpl");
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-     strcat(fileresvpl,fileres);
+   fflush(fichtm);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+   strcpy(pathr,path);
-       exit(0);
+   strcat(pathr,optionfilefiname);
-     }
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      and prints on file fileres'p'. */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
+   fprintf(fichtm,"\n");
-         for(j=1;j<=cptcoveff;j++)
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-         fprintf(ficresvpl,"******\n");
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+           imx,agemin,agemax,jmin,jmax,jmean);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldm=oldms;savm=savms;
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       }
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     }
-     fclose(ficresvpl);
+   /* 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] */
-     /*---------- End : free ----------------*/
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-   }  /* mle==-3 arrives here for freeing */
+   if (mle==-3){
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     ximort=matrix(1,NDIM,1,NDIM);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     cens=ivector(1,n);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     ageexmed=vector(1,n);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     agecens=vector(1,n);
-     free_matrix(covar,0,NCOVMAX,1,n);
+     dcwave=ivector(1,n);
-     free_matrix(matcov,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+     for (i=1; i<=imx; i++){
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       dcwave[i]=-1;
-     free_matrix(agev,1,maxwav,1,imx);
+       for (m=firstpass; m<=lastpass; m++)
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
-     free_ivector(ncodemax,1,8);
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     free_ivector(Tvar,1,15);
+           break;
-     free_ivector(Tprod,1,15);
+         }
-     free_ivector(Tvaraff,1,15);
+     }
-     free_ivector(Tage,1,15);
-     free_ivector(Tcode,1,100);
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+         ageexmed[i]=agev[mw[1][i]][i];
-     free_imatrix(codtab,1,100,1,10);
+         j=wav[i];
-   fflush(fichtm);
+         agecens[i]=1.;
-   fflush(ficgp);
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
-   if((nberr >0) || (nbwarn>0)){
+           cens[i]= 1;
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+         }else if (ageexmed[i]< 1)
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+           cens[i]= -1;
-   }else{
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-     printf("End of Imach\n");
+           cens[i]=0 ;
-     fprintf(ficlog,"End of Imach\n");
+       }
-   }
+       else cens[i]=-1;
-   printf("See log file on %s\n",filelog);
+     }
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-   (void) gettimeofday(&end_time,&tzp);
+     for (i=1;i<=NDIM;i++) {
-   tm = *localtime(&end_time.tv_sec);
+       for (j=1;j<=NDIM;j++)
-   tmg = *gmtime(&end_time.tv_sec);
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-   strcpy(strtend,asctime(&tm));
+     }
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     /*printf("%lf %lf", p[1], p[2]);*/
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+ #ifdef GSL
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ #else
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+ #endif
-   fclose(fichtm);
+     strcpy(filerespow,"pow-mort");
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     strcat(filerespow,fileres);
-   fclose(fichtmcov);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   fclose(ficgp);
+       printf("Problem with resultfile: %s\n", filerespow);
-   fclose(ficlog);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   /*------ End -----------*/
+     }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-    printf("Before Current directory %s!\n",pathcd);
+ #else
-    if(chdir(pathcd) != 0)
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     printf("Can't move to directory %s!\n",path);
+ #endif
-   if(getcwd(pathcd,MAXLINE) > 0)
+     /*  for (i=1;i<=nlstate;i++)
-     printf("Current directory %s!\n",pathcd);
+         for(j=1;j<=nlstate+ndeath;j++)
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   sprintf(plotcmd,"gnuplot");
+     */
- #ifndef UNIX
+     fprintf(ficrespow,"\n");
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #ifdef GSL
- #endif
+     /* gsl starts here */
-   if(!stat(plotcmd,&info)){
+     T = gsl_multimin_fminimizer_nmsimplex;
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     gsl_multimin_fminimizer *sfm = NULL;
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     gsl_vector *ss, *x;
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     gsl_multimin_function minex_func;
-     }else
-       strcpy(pplotcmd,plotcmd);
+     /* Initial vertex size vector */
- #ifdef UNIX
+     ss = gsl_vector_alloc (NDIM);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
-     if(!stat(plotcmd,&info)){
+     if (ss == NULL){
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-     }else
+     }
-       strcpy(pplotcmd,plotcmd);
+     /* Set all step sizes to 1 */
- #endif
+     gsl_vector_set_all (ss, 0.001);
-   }else
-     strcpy(pplotcmd,plotcmd);
+     /* Starting point */
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     x = gsl_vector_alloc (NDIM);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     if (x == NULL){
-   if((outcmd=system(plotcmd)) != 0){
+       gsl_vector_free(ss);
-     printf("\n Problem with gnuplot\n");
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-   }
+     }
-   printf(" Wait...");
-   while (z[0] != 'q') {
+     /* Initialize method and iterate */
-     /* chdir(path); */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     scanf("%s",z);
+ /*     gsl_vector_set(x, 1, 0.083); */
- /*     if (z[0] == 'c') system("./imach"); */
+     gsl_vector_set(x, 0, p[1]);
-     if (z[0] == 'e') {
+     gsl_vector_set(x, 1, p[2]);
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
-       system(optionfilehtm);
+     minex_func.f = &gompertz_f;
-     }
+     minex_func.n = NDIM;
-     else if (z[0] == 'g') system(plotcmd);
+     minex_func.params = (void *)&p; /* ??? */
-     else if (z[0] == 'q') exit(0);
-   }
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-   end:
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-   while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
+     printf("Iterations beginning .....\n\n");
-     scanf("%s",z);
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-   }
- }
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+ #include "hpijx.h"
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           oldm=oldms;savm=savms; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f",age);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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Removed from v.1.125
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	Added in v.1.166